I played vanilla Civ 4 and my thought then was "This game will be better than Civ III complete eventually, I like it a lot, but right now Civ III complete is still more fun."
Civ V will one day be better than Civ IV BTS but it's not there yet.
My two cents:
The AI needs fixing, it doesn't understand how to fight very effectively. It needs to be able to determine the best way to attack and then do it.
Diplomacy needs more consequences, a broken pact of cooperation or secrecy should penalize the happiness of the breaker, and your foreign advisor should be able to tell you who likes who and why, things such as "The Greeks and Iroquois have signed multiple research pacts, but Alexander is upset that Hiawatha keeps settling near his borders." This would be fun to read, help gameplay decisions and increase realism. I'm still stumping for an EU3 Causus Belli system someday in civ.
Rivers and trade posts need an update, and there needs to be a general rebalancing of improvements and tile yields. Buildings also need to be rebalanced to either cost a little less in hammers or be more worthwhile.
Great Scientist is overpowered. So are mounted units.
This is maybe the biggest and the easiest: Rework the Tech Tree. Make it so you need some prerequisites from other branches to keep researching. If I can't build a musketman I shouldn't be able to build an infantry.
Last, fix the lag time.
Other than that, so far a fine game, albeit still not as good as Civ IV BTS. But it will get there.