I know what I would LOVE to see in the game, and it wouldn't require a lot of coding either.
* Better distinction between planetary and civilisation bonus.
I'm probably just stupid, but sometimes I can't figure out if a wonder helps my entire civ, or just that planet.
Definetly. Planetary Influence/Loyalty is defined by "PrestigeBonus" and "ResistanceBonus" tags respectively in the XML files. Why not use those names? And Approval is already used in many places in the game as being Planetary Morale. Economy/Economics are at least different, but they can be easily mistaken for the other at first glance... I know I made the mistake of thinking the Mind Control Center only affected Planetary Economy and built it on my super-high class Economy planet. Not sure what do about the other few abilities that have planetary/galactic buildings that affect them, though...
But enough about that. Here's my short list of things I'd like to see in 2.0:
1. A little green "Earth-like" icon for the planets that are Habitable by All. I've been requesting this ever since DA's Beta though... so who knows. 
2. More Invasion videos. I'm suprised there's still only the few that were in the beta, honestly.
3. A Checkbox in the Upgrade for "Upgrade as many of this class of ships as you can afford" option. I hate having to upgrade ships one by one late game, and I feel like I'm wasting economic potential if I let my treasury float above 10k bc, let alone 20k bc. A "upgrade all ships of this class in this fleet" option as suggested earlier could work for me too.
4. Move all those various pop-up windows (Survey Findings, Asteroid Field warnings, "Pay-off for peace") to the GCN. Less clicking is good!
5. Constructor management tools would be a definate plus for me.
6. The AI needs to take better advantage of the new ship modules in its designs. Of course, any AI enhancements to ship design (and other things!) are very much welcomed. I typically restrict myself to only using the AI-designed combat ships just to put me and the AI on a more even level 
7. I'd really like to see the Orbital Defense Manager and its big brother dropped and just have all planets defended as though they had the Orbital Defense Manager. Of course, I have a (not fool-proof) work-around method for modding this in, if need be (Planet Quality Change is such a modder friendly ability...).
8. Speaking of Planet Quality Change... I kinda wish that when buildings with the ability are Upgraded/Destroyed that they would remove the extra tile(s). Would make the ability more useful for creating faux-galactic bonuses. Of course, you can get around this by just making the buildings not upgrade to each other... but that just feels clunky. 