I'd like to see...
-Revolutions and civil wars.
-Barbarians that settle down into civs over time.
-Artillery/air bombardment like that of Civ3, which can destroy buildings as well as units.
-Bring back the Senate! (but in a less intrusive form

)
-Civ-specific great people names.

-Babylon, the Iroquois or Sioux, Israel, Maya, and the Netherlands as new civs.
-2nd leaders for every civ.
-The Roman UU should be the
Legionary, not Praetorian, and America's either a B-29 or B-52.
-More realistic religions, including better spread so that the AI doesn't always pick Buddhism or Hinduism.
-Better U.N. system.
-Quantitative resources, including some that are produced by buildings!
and many others...
While some of these are already implemented in Civ 4 mods, IMHO they should be standard fare.
EDIT: Oh, and one other important thing I left out. A REAL EDITOR FOR A CHANGE! Not all this manually editing XML/Python crap. Civ 3's editor was pretty good, but I think the best would be a combo from Civ 2 and 3.