I view civ3 as "unbearably long" in the sense that, the game becomes very boring for me in the late industrial to modern eras. Civ4 needs to incorporate something to counter the pattern where the dominant civ power early on continues to grow in power exponentially (I think this is what people refer to as the snowball effect). Civs need to break up and collapse without all the losses being treated as gains to other civs - in other words, in civ3, a civ only dies when it is absorbed into another civ. The world as a whole is always increasing in power, tech, units, etc. I want Civ4 to depict prolonged global retardation!
And my suggestion for this is to have more powerful plagues, civil wars, famines, and any other ills. I also think the civs should be handicapped (perhaps through religion factor) so that the various regions bloom during different eras in a more historically accurate manner (this was not properly implemented in civ3 through the unique unit triggered golden ages).