I totally agree, that once you've passed the mid game and survived its very easy to beat the AI.
Now it's not easy to provide suggestions, because this definitely is caused by some mechanics AI uses and I can't say I perfectly understand them in Sins 2.
For example in Sins 1 the problem was the upkeep. AI was going fast to 2000 and their income was dropping drastically once you captured some fat planets, so once you kill the main fleet they had a hard time to rebuild it.
I see something similar here, at least I suppose it's something like this. I also see that after the main fleet is destroyed and you are taking ground - AI still wouldn't pump defences, bases can be barely developed on the from planets.
I also guess the AI should become smarter, and use the special abilities for scouting/scouts for identifying the weak spots (actually now the new AI is already much better in this department) and attacking key planets instead of trying to recapture. Also AI should become more evil, and instead of always taking the hard fight on the heavily defended planet - maybe jump to the next one (this way we maybe will finally use the jump inhibitors )
Also AI should be using the special abilities all the time they can and in a smart way (at least smarter way).
I also think that difficulty scaling should be done with more smart features activated for AI instead of giving them unlimited resources (is it still like this in Sins 2?)
I totally understand this involves some heavy work on the AI, but I think it's worth it.
Hope this helps!