So I'm not sure if this is already going to be in the game is some form but here goes.
Something that was a pain in GalCiv 2, especially in the second expansion pack, was the manually-assigned categories for each tech to guide the AI to go in a particular direction according to its needs.
Don't get me wrong, tech categories are a great way to get the AI to react to a changing galaxy, but they need to be dynamically created. For example, if a tech gives bonus ability points in say, Production and Economics, then it gets categorised under both of those.
Furthermore, when processing the tech tree, the information should be grandfathered along the branches. So if a tech which comes after a considered tech gives a bonus to Soldiering, the AI can see that the current tech leads to a bonus in Soldiering, which will be very handy when deciding how to defend against ground invasions or improve ground offensives.
Of course this makes a lot of assumptions about what will be in the new tech trees, but I thought I would throw it out there while it's fresh in my mind.