Just going by the movies, the ones in the prequels simply have larger numbers and better equipment (even if the OT walkers are better, they have fewer of them and less support vehicles and equipment).
The best Stormtroopers we've seen in the classic trilogy are the ones that go to Tatooine to look for the droids. We don't see a single one of them killed, but granted, we don't see most of their "battles." They were the best equipped and seemed the most elite.
The Stormtroopers are supposed to be better, but overall we see the Prequel era troopers in a much better light.
Then again Lucas says that the "modern" Stormtroopers aren't all from the same genetic stock of Jango (which supposedly made them all so uniformly great). So they could be better or worse. But ultimately the gear and equipment is the most important thing, and of course training.
As to the armor being "better" that's a matter of interpretation. On the one hand, the OT armor might be said to be "better" if it's more comfortable or lighter or something. But in terms of protection it doesn't seem to be any better. Blasters from both eras easily kill troopers. Are the blasters in the OT significantly stronger than the ones in the PT era? Who knows. But we do know that the handguns used both eras are adequate for taking out the armored troopers of that era. The armor doesn't seem that worthwhile for combat protection, at least not in the movies. That doesn't mean it couldn't be useful in other ways (like identification, NCB protection, etc) but you get what I'm saying I hope.