Nolan did do villains better than anyone else, before or since.
He was a bit uneven in that department from my point of view.
The Joker is of course fantastic, but it's mostly the performance from Ledge in my view as the writing was very weird at times (like the great opening scene ending with him getting away in a manner that fit the old 60s TV show, rather than a modern gritty movie).
Scarecrow was really interesting and using the horror style was inspired. Unfortunately he ultimately ended up quickly running away from Rachel, screaming like a girl, when he had finally fully come into his own element.
Ra's al Ghul was solid all the way through, so he's the best consistent performance in the trilogy for me.
Two-Face was someone I really disliked. Both how he came about and his look, plus how rushed it was, although I know many disagree with me. I really liked Harvey Dent though.
Bane was an interesting choice. There's some very good sides to him, but he also consistently made people laugh with his funny voice, and he was neutered in the end with the pointless Talia reveal.
Talia was just unnecessary to me.
Nolan is a great filmmaker, even more so outside Batman imo, but I don't think the villains were all that perfectly crafted in that trilogy. He definitely didn't deliver anything really bad, but there's some clear flaws with most of them so I don't think that really separates him from the rest.