I have no idea what they plan on things like starbases and other such mechanics. I haven't seen or heard anything with hints I could interpret. I blame Paul for being inscrutable.
I do expect continuing work on the AI. I think it will be incremental rather than dramatic, but every bit will help. As has been discussed, the higher level difficulties and extreme maps are not the primary demographic of the game, but Brad being Brad and Stardock being Stardock, the overall quality of the AI is a point of pride that will be pushed continuously and steadily for a long time.
I expect continued polish on the overall economy mechanics. I am pretty sure that is a high priority topic with Paul, along with a few million others, of course. I worry that it will mostly be little nerfs that annoy people, but Paul has shown some creativity with his balance skills so that may not be so bad. I feel that the tech pace and values need some more adjustment as well, but expect only minor things there if any.
I hope for AI fleet skills. This will be very important for those whose demographics are into challenges as much as any roleplay. I also think it will help the battle viewer be more interesting as ship roles and fleet composition are fine tuned, the mechanics should start affecting the on-screen behaviors. (I am a big fan of the battle viewer, by the way. I like eye candy like that as well as all the challenges. More eye candy, please!)
Because of forum feedback, I am also expecting a lot of UI work. Or at least hoping.
Beyond that, I leave the guessing to the psychics. 