I want units to have a bag of holding and be able to carry around items, I want abilities like spells (healing/attack/storm/hide/etc.), weapons, grenades, etc., hmm maybe, since we're at it, to be able to replicate a T-1000 would be awesome, we'd need to integrate the PediaIcons.txt and the .ini files into the .xml format of the scenario itself so we can describe the abilities and specify the animations for each
Having trolls be killable only by fire or acid like in Faerun would be good as well.
Seriously?
More traditionally civvy stuff:
Having new factions emerge after the game is started, having units, cities, tiles, etc. change ownership to and from these emergent factions.
Having units just sprout from the ground to simulate an invasion, maybe even programmed to attack a city or other place.
Making culture no longer be the only method of expanding tile ownership. Populational growth itself is an obvious one, purchasing tiles from foreigners is another one.
We could buy a city-state for the entire value of its buildings and units, eh? We could also buy its vassalage for a smaller sum.
New forms of diplomacy, like Protectorates, Non-agression Pacts, improved embargos instead of the crap civ3 has, being able to trade any sort of units as well as the forementioned land purchase; general improvement of the Diplo workings so that you don't end up like in CivIII where anything you do maks you take a rep hit and anything the AI does makes you take a rep hit;
Water terraforming!
Bridges!
We could have two cities on either side of a river be merged into one!
Changing the properties of a tile itself with time, so you can only settle a place or build a road on it during a certain period -or only in the summer if we put in an optional season mechanism-. The sky's the limit!
We should probably look at getting the basics in first, some of these are quite advanced. Only trouble is not many testers around these parts.
QFT. Dropping stuff on death could be interesting, for example, in pirate scenarios.
Nice idea!