Actually I've also noticed that the AI rolls over at a certain point too. But I don't think it has to do with the fleetcommanders.
After you take enough systems, the AI is limited greatly by the galactic population (thus reducing its economic advantage), it loses the ability to build more ships. The AI also seems to like to attack with large numbers of capital ships, which is fine and makes for good battles. However, I suspect that this combination leads to the AI becoming passive in late game situations, as the AI's frigates and other ships that can be built from light and heavy shipyards are still sitting around, taking up galactic pop. Then after you take away a lot of the capital shipyard systems from them, they're left with the option of only building frigates, and in the case of the NR, fighters. The AI seems to then decide that these are underpowered fleets that can't quite go toe to toe with your capital ships, so it neglects to attack.
In my experience, by the time you hit this point, you really do own a colossal advantage anyway. I mean do you really enjoy taking on an NR fleet that has 70 E-Wing squadrons, 20 CR90s, and some Marauders? It might seem funny but at that point, the GC is pretty much over, you've won.
I think you are right, it is not the fleetcommanders.
The vanilla game does the same.
When the AI stops attacking the game is more or less over. The thing that strikes me is that when it still has for example 40% of the planets it attacks like crazy, and then it looses one more planet and it is over. A human player wouldn't quit, but the AI can probably calculate when it becomes pointless to continue.
In the hunt for Zsinj GC playing as the IR if you capture Kuat right a way, The AI is left without a level 3 space station. And without capital ships it is indeed rather embarrassing to see the NR attacking with all those small ships.
But if you have 40 preybirds you can take on quite some capital ships.