Probably it would be a good idea to make a list of all basic stuff that was in SMAC, but that was left out of Civ3. If I could, I would make such a list myself, but the problem is that I don't have Civ3 - I sold it one month after first buying it myself. So some help from someone familiar with both SMAC and Civ3 would be appreciated!
IIRC these are at least a few things I can remember:
1> Bring back the ability of units of allied civilizations (pacted factions in SMAC) to be on the same tile.
2> Allow transfer of unit control between friendly factions/civilizations
3> Bring back the ability to ask a civilization to stop a war.