You're kind of comparing bell peppers to chili peppers here. They're both peppers but they're not really the same thing.
Both of them, I think, are the best of their Castlevania "type".
That being said, I'd have to say Rondo, just for the fact that I've played it more. That's mostly because I'm a Classicvania kind of guy though. I like the feel of Rondo. It's very twitch, Richter is very heavy, I love the music, and just feel overall more accomplished when I beat it.
That being said, SotN IS longer, so it would make sense I haven't beaten it as much.