system
Given the following post, respond as if you're commenting on Reddit:
human
[Star Trek] What's the benefit of some ships having more that two nacelles, and why aren't all ships like built like that?

All of the flag ships have only had to nacelle but there are a few ships with three or more and some with only one. why the variance?
gpt
You only need 1 set of warp field coils to make a warp field and move FTL.  So 1 nacelle would work.  However, for maneuvers you need 2 nacelles so that you can vary the field strength to turn the ship.

From the TNG:TM

>Second, a pair of nacelles is employed to create two balanced, interacting fields for vehicle maneuvers. In 2269, experimental work with single nacelles and more than two nacelles yielded quick confirmation that two was the optimum number for power generation and vehicle control. Spacecraft maneuvers are performed by introducing controlled timing differences in each set of warp coils, thereby modifying the total warp field geometry and resultant ship heading. Yaw motions (XZ plane) are most easily controlled in this manner.

We do see some ships with 4 nacelles.  The Constellation class had a 4 nacelle configuration.  That class was a very long range exploration vessel and the extra nacelles were most likely for redundancy.  Other examples such as the Prometheus class had multiple nacelles because it could separate into multiple independent vessels. 

Apparently there are some additional odd number configurations in alternate timelines.  One being a creation of Q so it is hard to say if that was a "real" possibility.  In another we don't really have enough information to know what is going on.

(Also, just a small thing, most ships we see on screen are not flagships.  Of the Enterprise's only the Enterprise-D is called the Flagship of the Federation. In a more traditional sense of a flagship commanding a fleet, we see the Defiant in that role a few times.   The vast majority of ships are dual nacelle (even non-federation designs))