OK, here's what I've noticed, some of obvious, some of it not. (Noble, Standard, Epic, fwiw.)
1. Map options. Balanced resources for one, and different world wraps (Oasis with Toroidal is a lot less frustrating.) Resource allocation also seems to favor capitals less heavily than before, at least on the Normal setting. Lots more Desert than I recall, but that could just be perception.
2. Different AI priorities, especially with techs. Tokugawa beat Izzy to Buddhism in one my games! The race to the early religions seems less tense, as well as early wonders. Most of the early wonders are there for the taking, but beware the waves of Barbs, and AIs that build huge militaries early on-- early war against Shaka doesn't seem to be the best move.
3. Barbs, Barbs, Barbs. Smarter, more of them, and they don't like city life any more. The Great Wall is an essential wonder for the warmonger, IMO, since it will free up easily a half dozen units on maps (Great Plains, Lakes, etc) where they can come at you from all four directions. Barb cities also seem to spawn closer and more frequently than before, but again, this is a casual perception.
4. Some of the AIs are cottaging a little more, but it's still a farmer's paradise for most of them. They also still hoard Great People for Golden Ages, unless there's a tech or religion up for grabs.
5. Less AI trading in the midgame. Before, there would seem to be only one civ (like Monty) that was woefully behind; now, there might be two or three out of the six on standard settings. Haven't packed a map with extra civs yet to see how many fall behind in a crowded setting. If SS is your goal, chances are I'll only have one serious competitor-- maybe. Seems to be different from Vanilla, or maybe I'm just getting better. May be time for a game on Prince.
Hope that helps, and anyone who disagrees feel free to chime in.