Two things.
First a new victory condition: Military victory does not count. Which is to say that if you're the only civ left at the end, you don't win the game, you lose.
The idea being to force players to go for the other victory conditions, and allow for a less combat oriented game.
Second, an improved political system. I don't know about these councils and whatnot, but what I do think should be done, is in single player games (And multiplayer games with AI factions) the AI should track your actions and basically have a "rating" for you, based on whether you break your alliances or keep them, whether you attack other factions or only fight in defense, and other things of that nature. There should be no mega evil empire flag, but rather, if you've expanded through a great deal of offensive warfare, breaking treaties, and (Most importantly) surprise preemptive attacks, you will be looked at badly (Except by berserker races) and other races will be inclined to shoot first and ask questions later. Whereas if you've been "good", other races will treat you peacefully except for berserker races (You'll still want to keep your distance from the xenophobic races too).
This allows for a "realistic" or "idealistic" game (Depending on your point of view) where you play through the game only making retaliatory attacks, and can still win through the specific victory conditions of your game.
The other thing I think should be added, is a federation alliance level. If you've played Starships Unlimited you'll be familiar with the concept... It's an unbreakable alliance that fuses two races together permanently. In multiplayer that means that both players have communal control over their units and planets. In single player it would mean the AI basically gives up control of it's units to the player.
Just another option for diplomatic victory, and playing as a nice guy