In addition to what already have been said, I would add that I haven't seen AI use higher tier doctrines (like assault\scirmisher) and all these new modules, like nano-repair, scramblers, etc.
I imagine if AI was trained to build their fleets in pyramid structure, with big\huge hull ships always being a priority and cruisers\frigates supporting them it would make the game more challenging\interesting.
I think the belief that bombers are somehow good has to go, They are not, especially not in the mid\late game. Even in big numbers and even with cheesy tactics like shield bubble (which AI doesn't use of course). Especially given that only 1 tiny ships can be produced each turn and high difficulty AIs waste a lot of production on them. Bombers\fighters could be somewhat relevant if there was such thing as tracking in the game, when bigger ships with bigger guns would have a hard time hitting tiny ships. But there is no such thing, so they become useless almost from the start of the game, when you can build frigates.
I really hope Stardock addresses AI issues, because as soon as the game stops being challenging, it soon stops to be interesting to play.