I greatly enjoyed playing CTP 2 before civ 3 came out, and I fully share the opinion that many features of CTP would greatly enhance the gameplay of civ. It just seemed as such a regression in civ 3 to go back to one-on-one combat again (except for armies, lame rip-off). The combined army, crude as it was, actually made a alot of sense, and also encouraged to fill up your army with various kinds of units to perform different functions.
I know civ 4 also encourages you to do this, but for a different reason. For offensive stacks, it's simply necessary to include some defensive counters for fear of your stack being wiped out by the one type of unit it is vulnerable to.
Also greatly missed are the diplomatic attitudes when in contact with leaders. I'll grant you that it was probably something which worked rather crappy, but I just loved the possibility to convey my opinion of my rival civs when in contact with them. Now only the AI gets to bully you or coddle you. I wonder if the AI actually ever considers what my opinion of it is... does it reckon that bombarding me with demands will sort of increase the chances that my army will pay their cities a visit soon?
Anyway, back to CTP. The public works system, once used to it (as it works quite different from the worker system), really is nice and easy. As others said before, having to instruct all your workers to do what is obvious to anything but an automated worker just gets tedious.
CTP also had several units which I think are sort of missing in the civ game. Many non-combat units of course, but also things like the industrial age transport ship. Now we have to keep using galleons until we have transports.
Final feature which I really liked, but I know that many civ players also want none of it, were the future eras, the genetic and diamond age I think. I don't mind if civ goes a bit off the wall and into the what-if. For the same reason that I would like to see ethnically diverse units being extended into later eras (or are canons only ever operated by white, presumably european people?), I like adding a bit of sci-fi with future buildings and units. The next-war mod is a joke. It's broken on all sides and really doesn't include that much new content. There's this genetic era mod which is quite cool, but I think that the BtS expansion could have done with a scenario less, and a more extensive future eras mod instead, allowing you to play from the stone age to the diamond age.