On those areas Brad mentioned in GalCiv 2, he did pick on the weak areas of a very good game. One thing I've noticed, I tend to be much more harsh and vicious on a game the better it is for some reason. It's like I can forget a game if it's crap, but a really good game- those things keeping it from greatness I'll really scrutinize and be difficult about.
I have my own biases also. I tend to strongly dislike inelegant design and weak AI.
GC2 Diplomacy was better then most games to me, with the exception of minors and the UP, which were dreadful. Also, the Research/Economic treaties felt a bit tacked on, and this became really apparent in Elemental, and I've been very critical of that.
GC2 Tactical Battles would have been nice, but weren't a necessary part of the design. I'd like to see GSB-style tactical battles in GC3 personally, where you do your setups, then the ships battle based on pre-battle orders. I'd also have liked to have seen a retreat option to try and save a losing fleet after it becomes obvious you can't win (speed would be critical here). As for Elemental tactical battles- I think AOW-style tactical battles were awesome, but wouldn't work as well with Elemental. With Elemental, I'm unsure what would work best, but I'd want the individual troops, even in a group to be unique, and have skills/stats that impact the battle as heavily as the armor/weapons. This is in addition to an actual working tactical AI.
I wouldn't really want quests in GalCiv to be quite honest. The Events/Alignment in GalCiv- which I consider the equivalent of Elemental Quests- should have been handled with a EU-style trigger system. I think EU3-style government sliders and style of doing events of all games could have been a good influence on GalCiv 2/would be a good influence on GalCiv 3. Elemental Quests- needs a revamp, will get one in FE, will withhold judgement until then.
The UI in GC2 was fine, except for the entire starbase/constructor part of the game- where it was dreadful. the UI in Elemental is dreadful right now , though 1.19 looks promising and should fix a number of my complaints.