I highly prefer Colonization to all the Civilization episodes I have played. Colonization feels more focused, more tangible, and yet still manages to be a great management game with credible threats with multiple parties: natives trying to fight back for their land, other European powers trying to establish successful colonies on their own, and ultimately the royal power you will fight against to secure your Freedom.…
The Rise of Revolution mod for Civ4Col is a little better (it's also just really good in general, aside from being better about its recognition of marginalized people), but...there is a fundamental "ick" to colonizing other people's shit that I don't think this game properly grapples with. Because there's a moral issue to European colonization, and while I can see that being surfaced very well in a hypothetical game (I noodled on one for a while) I don't think either Colonization or Civ4Col even tries. And that's a real shame.
[1] - Yeah, you can go play the Spanish and knock over a bunch of native settlements. But you almost never will after you get to a certain level of play. Instead, you will find yourself near the Arawaks or whatever, who have their AI ramped up to turbo-aggressive, and suddenly you'll just have to roll out your army at them, it's not your fault, it's not your fault, it's not your fault...ew.