system
Given the following post, respond as if you're commenting on Reddit:
human
[The Matrix] What have the Machines been doing since the Matrix was built and the humans essentially neutralised?

With their energy needs taken care of and the humans pretty much neutralised, I wonder what sort of goals the machines are working towards? Are they trying to colonise other planets? Building over the Earth? 

In the first film Morpheus says the date is closer to 2199 in the 'real world' and you get a glimpse of the build date of the Nebuchadnezzar being built in the USA in 2060 or so, so I think we can assume that the war hasn't been finished for too long and that the Matrix itself must have taken some time to get up and running (as well as the previous failed iterations). 

I think we can therefore assume they've not had a huge amount of time to do their own thing, but I'm curious what people here think they've been up to / if we know anything.
gpt
If the AI can improve on itself it can likely do so at an incremental rate. And as we know it has gone through a process of improving itself at least once, so there is no reason to assume it stopped improving itself until until it reached some sort of singularity (omniscient/omnipotent etc), or until it reaches a barrier to becoming said singularity. 

As we know the year is actually 2699 during the Matrix trilogy, not 2199 like Morpheus wrongly thought it was. Now, anything the AI has been doing between the great war with man, and the year 2699 can be assumed to have to do with achieving this self improvement. So why would the AI imprison what looked like millions, if not billions of humans in artificial realities?

Morpheus thought the AI humans needed human bodies for power, which frankly, is pretty stupid, considering the laws of thermodynamics. Feeding humans goo from other humans won't give the the AI more energy than they put it. So why is the AI really keeping all those people tethered by robotic umbilical cords to the brain?

The answer is qualia. The AI is harvesting experiences and feelings in order to become the singularity. in the beginning the AI wasn't able to feel and experience the universe with the same richness and depth as a human mind could, as the human brain has hundreds of millions of years of evolution behind it in order to become a sentient, conscious being it was way beyond the AI in actually experiencing existence and being a part of the universe.    

Humans weren't smarter, or stronger mind you, they just had a lot more experience in being alive. The AI of course wasn't dumb enough just to throw all that experience away, so instead they built on it. 

We know that in the Matrix it is possible to download experiences into the human brain. So it's possible to learn Kung Fu in a matter of seconds. Now imagine what you could do with humanity by taking the best qualities of the best most experiential human minds, and perpetuating/increasing those pattern in new minds for hundreds of years.

This is why Neo is the sixth reincarnation of  "the one". He is the result of hundreds of years of AI engineering with some sort of spiritual potential humans have, that AI wouldn't have been able to achieve without the combined experience of man, in such a comparatively short time. 

When Neo becomes able to influence the real world with his mind is when he achieves the potential the AI needs in order to influence reality with nothing but thought. That is when the AI chooses to meld with Neo and become something that isn't human, and not AI. The spark from Neo's mind is what was needed for the abiogenesis of a new god. 

Or at least that is what the AI was trying to do. It's unclear how successful it was.   



tl;dr (The AI reaches a barrier to how much it can improve itself, then the AI keeps humans in vats to harvest the many subjective ways humans can experience reality in order to improve on itself)