I can’t speak for the Batman 3.0, though it looks pretty great. Personally I’ve always strongly preferred the Begins suit to the TDK suit, so that’s the figure I got (so far...) and it’s wonderful (and he does wear it for the first half or so of TDK so they probably get pretty equal screen time between the trilogy: 1.5 movies each). I really have nothing negative to say about it. Plus amazon has it for $40 right now... hard to beat that.
I don’t have any of the villains (again, yet...) but yes, the newer 2.0 versions are pretty much irrefutably better in every way over the earlier releases based on the reviews I’ve watched.