user9943: I have been observing the rampant closing of questions based on being a duplicate of "If a trait would be advantageous to an organism, why hasn't it evolved?".  I am of the opinion it is currently being (ab)used as an invalid reason to bury valid questions.  Not only that, it's overuse is turning it into a cliche.  I appreciate the efforts from the community that have gone into this question, but as of now other questions are being funneled into its webs without solid reasons.
Specifically, the community question deals with "Why not?", and not with "Why?".  Of course, the community question is great to close questions like why eagles don't have jet engines and leopards don't grow shotguns.  But the argument that it answers the "Why did X evolve" is incorrect, and hence its use is being quite inappropriate at times.  For example, take the recently closed question "Why do insects have 6 legs?".  How on earth do the answers of "If a trait would be advantageous to an organism, why hasn't it evolved?" answer this question?  OP did not ask why insects didn't evolve 7 legs because the 7th would make a nice spare.  Instead, OP asked a valid question why 6 appendages is so strongly selected for.  The speciation in the animal Kingdom is extreme in the Insects. And the fact they all have 6 legs is henceforth a valid lead to look for its benefits.  That is not only a valid question, it's an awesome one.  To see this mod-closed based on flawed grounds makes me sad.  Please, stop this aberrant use and clichefication of "If a trait would be advantageous to an organism, why hasn't it evolved?"  
EDIT - To add an example where the community question is appropriate IMO: What, if anything, would prevent flying fishes evolving to be capable of extended flight?. This question is highly hypothetical and suitable to be closed as a duplicate of the community question. Some people question the difference between the community question's "Why not" versus "Why" nature. The insect question is "Why?", which is a valid question. The flying fish question is a "Why not". The latter, IMO, would be a definite target being a duplicate of the community question, being hypothetical and speculative in nature. The 6-appendage insect question is based on an existing phenomenon, namely a highly conserved body plan of insects.    

user10456: I disagree that this question is an invalid duplicate close. 
The final sentence of the question

If it's an advantage either way, why don't bigger life forms like
  mammals have 6 limbs?

makes the intent of the question pretty clear. It is essentially asking "Why didn't insects lose 2 of their legs / Why didn't animals gain 2 legs if it is advantageous for them to do so?". 
The final question (as well as the bulk of the original text) can be easily answered by the "Advantageous trait" question. While your answer was an excellent answer that explained a benefit of the dual-tripod gait, the gait is clearly unnecessary for easy locomotion, as can clearly be seen in all the animals with other numbers of legs that are not multiples of three. bshane's answer covers this in better detail. 
While it is true that the dual tripod gait does provide significant stability benefits, the stability is not required for locomotion, and IMO likely evolved after the ancestral insect had its Hox duplication, giving it six legs. 

user1578: TL;DR
I think that "Why did feature F evolve in organism O" is always a bad question. However, in some cases it does hide a good question. So, let's get rid of the bad questions - but if there is a good one hidden, reword to unearth that one.

In more words
I don't currently see it as overused. But I certainly see your point that we don't want to get rid of all questions which can fit this schema. My view is that something should be done about the "Why did" questions too, because:

Many of them share the same problem as the "why not" questions
Some of the "why did" questions can indeed produce a very interesting answer. But if they do, it is an answer to another question.

The problem
The problem behind "why did feature F not evolve in organism O" is clear: evolution does not have motives. But the "no motives part" actually also covers the "why did F evolve in O". I trust that all our regular users know how it goes, but I'll repeat it - a feature can evolve because there is selective advantage in having it, or because there is no selective advantage against not having it. The second reason makes for lousy "why" questions. In the first reason, an answer saying "because there was selective advantage for it" is a boring answer. The interesting answer comes when we explain what role does F have in O, which as a side effect makes it so amazing that there is a selective advantage for it.
The "why did evolve" question is actually a layer of misdirection. It allows a false assumption to take place ("If it has evolved, there must have been a selective advantage for it, so the two questions are equivalent").
My suggestion
We can look through the uninteresting layer of "why did" and reveal the real question beneath it. Reword "Why did F evolove in O" into "What role does F play in O?"

Sometimes, it will have a good answer, and it will be the same answer as to the "why did it evolve" formulation. Compare the answers to "why did an opposable thumb evolve in humans" and "what is the role of an opposable thumb in humans".
Sometimes, the answer will be a simple "none". If this is so, the formulation (or the trouble finding it) may help the asker realize this. Compare "Why did the humans evolve an urethra going through the prostata" from this question, to a possible rewording such as "What is the role of the piece of the urethra which goes through the prostata in humans". This sounds a bit weird, but there is no real way for a layman to know that there is none, so I guess people could ask it, so we can give a simple answer.
Sometimes, the answer will be a "none", and really obvious. Imagine somebody who wonders "why do we have 5 fingers, and not 4 or 6". He'll be forced to write the question as "What is the role of the human fingers?". With some luck, he'll notice himself that all of the points would apply to 4 or 6 fingers, and won't bother us with "but why exactly 5?". If he asks it nevertheless, and we have to correct him, this might be the critical piece of information which makes him grasp how evolution works and how it doesn't.

As a bonus, this will spare us from repeating every single time that evolution is not a human engineer and does not go around thinking up optimal solutions. We can still point to the canonical "why not" question when editing to reword, with the suggestion that the OP reads it in order to get background knowledge.

9943: <p>I have been observing the rampant closing of questions based on being a duplicate of "<a href="https://biology.stackexchange.com/questions/35532/if-a-trait-would-be-advantageous-to-an-organism-why-hasnt-it-evolved">If a trait would be advantageous to an organism, why hasn't it evolved?</a>".  I am of the opinion it is currently being (ab)used as an invalid reason to bury valid questions.  Not only that, it's overuse is turning it into a cliche.  I appreciate the efforts from the community that have gone into this question, but as of now other questions are being funneled into its webs without solid reasons.</p>

<p>Specifically, the community question deals with "Why not?", and <em>not</em> with "Why?".  Of course, the community question is great to close questions like why eagles don't have jet engines and leopards don't grow shotguns.  But the argument that it answers the "Why did X evolve" is incorrect, and hence its use is being quite inappropriate at times.  For example, take the recently closed question "<a href="https://biology.stackexchange.com/questions/39203/why-do-insects-have-6-legs/39210#39210">Why do insects have 6 legs?</a>".  How on earth do the answers of "<a href="https://biology.stackexchange.com/questions/35532/if-a-trait-would-be-advantageous-to-an-organism-why-hasnt-it-evolved">If a trait would be advantageous to an organism, why hasn't it evolved?</a>" answer this question?  OP did not ask why insects didn't evolve 7 legs because the 7<sup>th</sup> would make a nice spare.  Instead, OP asked a valid question why 6 appendages is so strongly selected for.  The speciation in the animal Kingdom is extreme in the Insects. And the fact they all have 6 legs is henceforth a valid lead to look for its benefits.  That is not only a valid question, it's an awesome one.  To see this mod-closed based on flawed grounds makes me sad.  Please, stop this aberrant use and clichefication of "<a href="https://biology.stackexchange.com/questions/35532/if-a-trait-would-be-advantageous-to-an-organism-why-hasnt-it-evolved">If a trait would be advantageous to an organism, why hasn't it evolved?</a>"  </p>

<p><strong>EDIT</strong> - To add an example where the community question <em>is</em> appropriate IMO: <a href="https://biology.stackexchange.com/questions/40006/what-if-anything-would-prevent-flying-fishes-evolving-to-be-capable-of-extende">What, if anything, would prevent flying fishes evolving to be capable of extended flight?</a>. This question is highly hypothetical and suitable to be closed as a duplicate of the community question. Some people question the difference between the community question's "Why not" versus "Why" nature. The insect question is "Why?", which is a valid question. The flying fish question is a "Why not". The latter, IMO, would be a definite target being a duplicate of the community question, being hypothetical and speculative in nature. The 6-appendage insect question is based on an existing phenomenon, namely a highly conserved body plan of insects.    </p>
 10456: <p>I disagree that this question is an invalid duplicate close. </p>

<p>The final sentence of the question</p>

<blockquote>
  <p>If it's an advantage either way, why don't bigger life forms like
  mammals have 6 limbs?</p>
</blockquote>

<p>makes the intent of the question pretty clear. It is essentially asking "Why didn't insects lose 2 of their legs / Why didn't animals gain 2 legs if it is advantageous for them to do so?". </p>

<p>The final question (as well as the bulk of the original text) can be easily answered by the "Advantageous trait" question. While your answer was an excellent answer that explained a benefit of the dual-tripod gait, the gait is clearly unnecessary for easy locomotion, as can clearly be seen in all the animals with other numbers of legs that are not multiples of three. <a href="https://biology.stackexchange.com/a/39211/10456">bshane's answer</a> covers this in better detail. </p>

<p>While it is true that the dual tripod gait does provide significant stability benefits, the stability is <strong>not required</strong> for locomotion, and IMO likely evolved after the ancestral insect had its Hox duplication, giving it six legs. </p>
 1578: <h1>TL;DR</h1>
<p>I think that &quot;Why did feature F evolve in organism O&quot; is always a bad question. However, in some cases it does hide a good question. So, let's get rid of the bad questions - but if there is a good one hidden, reword to unearth that one.</p>
<p><a href="https://i.stack.imgur.com/VVt6p.png" rel="nofollow noreferrer"><img src="https://i.stack.imgur.com/VVt6p.png" alt="enter image description here" /></a></p>
<h1>In more words</h1>
<p>I don't currently see it as overused. But I certainly see your point that we don't want to get rid of all questions which can fit this schema. My view is that something should be done about the &quot;Why did&quot; questions too, because:</p>
<ol>
<li>Many of them share the same problem as the &quot;why not&quot; questions</li>
<li>Some of the &quot;why did&quot; questions can indeed produce a very interesting answer. But if they do, it is an answer to another question.</li>
</ol>
<h2>The problem</h2>
<p>The problem behind &quot;why did feature F not evolve in organism O&quot; is clear: evolution does not have motives. But the &quot;no motives part&quot; actually also covers the &quot;why did F evolve in O&quot;. I trust that all our regular users know how it goes, but I'll repeat it - a feature can evolve because there is selective advantage in having it, or because there is no selective advantage against not having it. The second reason makes for lousy &quot;why&quot; questions. In the first reason, an answer saying &quot;because there was selective advantage for it&quot; is a boring answer. The interesting answer comes when we explain what role does F have in O, which as a side effect makes it so amazing that there is a selective advantage for it.</p>
<p><em>The &quot;why did evolve&quot; question is actually a layer of misdirection</em>. It allows a false assumption to take place (&quot;If it has evolved, there must have been a selective advantage for it, so the two questions are equivalent&quot;).</p>
<h2>My suggestion</h2>
<p>We can look through the uninteresting layer of &quot;why did&quot; and reveal the real question beneath it. <strong>Reword &quot;Why did F evolove in O&quot; into &quot;What role does F play in O?&quot;</strong></p>
<ul>
<li>Sometimes, it will have a good answer, and it will be the same answer as to the &quot;why did it evolve&quot; formulation. Compare the answers to &quot;why did an opposable thumb evolve in humans&quot; and &quot;what is the role of an opposable thumb in humans&quot;.</li>
<li>Sometimes, the answer will be a simple &quot;none&quot;. If this is so, the formulation (or the trouble finding it) may help the asker realize this. Compare &quot;Why did the humans evolve an urethra going through the prostata&quot; from <a href="https://biology.stackexchange.com/questions/40503">this question</a>, to a possible rewording such as &quot;What is the role of the piece of the urethra which goes through the prostata in humans&quot;. This sounds a bit weird, but there is no real way for a layman to know that there is none, so I guess people could ask it, so we can give a simple answer.</li>
<li>Sometimes, the answer will be a &quot;none&quot;, and really obvious. Imagine somebody who wonders &quot;why do we have 5 fingers, and not 4 or 6&quot;. He'll be forced to write the question as &quot;What is the role of the human fingers?&quot;. With some luck, he'll notice himself that all of the points would apply to 4 or 6 fingers, and won't bother us with &quot;but why exactly 5?&quot;. If he asks it nevertheless, and we have to correct him, this might be the critical piece of information which makes him grasp how evolution works and how it doesn't.</li>
</ul>
<p>As a bonus, this will spare us from repeating every single time that evolution is not a human engineer and does not go around thinking up optimal solutions. We can still point to the canonical &quot;why not&quot; question when editing to reword, with the suggestion that the OP reads it in order to get background knowledge.</p>
