I don't love SMW at this point, kind of find it too easy, and I never liked all the food themes/dinosaur design stuff. The only thing that really stands out about that game to me from the series is the secret/map path structure, which has yet to be topped. Otherwise I much prefer the vibe of SMB3.
I think Mario 64 can't be undersold, particularly if you hadn't grown up with 3D games. It didn't just invent 3D platformers, it invented 3D games, and was also incredible on the fundamentals. Playing that for the first time was like seeing a movie in color for the first time (or some better analogy).
Past that, I agree that Rogue Leader was awesome. Beautiful, chock full of content, played great, lots of challenge if you wanted it, tons of unlocks. It's kind of a wonder that the studio was never able to make anything decent again.