I can think of absolutely nothing that has become more complicated going from 2e to 3e.
Combat is even simpler, if you consider how entangled it had gotten with the Skills & Powers rules subset, which, let's face it, a lot of hardcore gamers used and/or tried to use.
If I had to pick a spot where 3e has gotten hairier, it would have to be feats, and the keeping track of them in combat. Character development with the goal of picking up a prestige class might be another, but I don't use PrCs in my games; although they are really no worse than the stupid kits from 2e ...