Super Mario World 2, in almost every category I can think of.
SMW2 has THE best level design I've ever seen in any platform game I've played. 2D or 3D. Especially when you play for 100% on every level. Not knocking on SMW1, as it had great levels also, but SMW2's are just brilliant. I also like SMW2's graphic style a bit more. I mean, I know it came out a lot later, but still. I have also perfect cleared (96 goals) SMW1 in about 2 hours 10 minutes -- in one sitting. SMW2 takes me a LOT longer to clear, even just speed running without regard to score.
One thing I do like more about SMW1 is its level select screen. My sole gripe with YI is that it's quite a bit linear. You have to play 48 levels in the same order every time you beat it. SMW1 has literally dozens of paths you can take to beat the game.