Heh, Ill be really disappointed if at least civ start locations & flat maps aren't added to the editor in a patch

More like feel cheated on that one
Things I'd like to see in an add-on though

1) MP, duh

2) Scenario editor, placable units, scripting etc.
3) A more flexible map generator. The ability to say I want 3 continents, X players per continent, X sources of iron (spread out or clumped) etc. This is pretty important for good multiplayer games, that or we'd just have to rely on pre-made maps.
4) A 5th age. This is where terraforming techs would come in along with area 51 style aircraft

5) Great Leaders that arent from conquest. Maybe one of your scientists becomes an Einstein or Newton (if your using scientists citizens that is) or something when you get a certain advance.
Really you could have military leaders, scientists, philosophers, artists/musicians (other culturial leaders), political leaders, etc. Obviously only the military type should be building armies. Though it makes about as much sense for a Edison great leader to build an army as the ones we have now finishing cure for cancer in 1 turn

6) More diplomacy, alot of whats mentioned above is good.
7 ) I like the colony stuff listed above. Id just have them all automatically given colonies or airports though rather than trying to give them a build key. Also they don't need a culture border so much as being immune to assimilation if garrisoned. At least immune to the automatic assimilation

8) Cities shouldn't culture "flip", they should revolt though. And by revolt, I mean every foreign citizen point should be able to convert into 3-5 revolutionary units (5/4/1 roughly, though varying by age), that have a simple deterministic AI to take the city, then they rejoin the old civ. Cities in revolt should also be subject to random sabotages to their production or garrisoned units (damage).
9) The option to make bombardment of any unit lethal in the editor on a unit by unit basis. I actually hope this is patched in.
10) Civil wars in civs when player slots are open. They'd be rare, but it'd be interesting if your peaceful French neihbors once ruled by the benevolent Joan of Arc suddenly split and came under the control of Napolean. Or more extreme Catherine to Stalin or such

11) Im dreaming here, but it'd be awsome if they tried birth of the federation (which I didnt really like though I am a star trek fan, it was just pretty bad compared to moo2) and did something like the minor cultures system it had. Basically instead of having 16 players in the game, you'd have 50-60, but only 5 or 6 of them would really be allowed to expand. It could be achieved by just giving the "lesser cultures" a very limited AI and setting severe building limits on them (like say < 5 cities and 10 units). You should still be able to enter normal diplomacy with them though by contacting one of their units on the map or maybe double clicking on one of their cities. It'd just be something to add alot of spice to the game, beyond treating all lesser cultures as goodie huts or barbarian villages ;P Also a lesser tribe should have limits to its culture expansion, and allow even their capitals (if they even had them) to be assimilated, so by late game they'd start to vanish except in remote parts of the world.