Agreed. SMB3 is, I still maintain, the single best game ever created.
Though you're right, ALttP is amazing (as is Link's Awakening on GB).
I think at the end of the day, this just really isn't a fair question, because each one of these series bring so much different, and so much good. I mean for christ's sake, the first entry in each series literally just about founded each gaming genre
SMB - Side-Scrolling Platformer
Zelda - Free Roaming Adventure
Metroid - Free Roaming Action
All three were so innovative for their time, it was ridiculous (ridiculously awesome, that is).
I just wish Nintendo would finally make a Star Tropics 3, and make it AWESOME. Don't make it with 3D polygon graphics, just standard, overhead, 2D sprite based for me thanks. I wouldn't object to, say, a 16bit type of style. But otherwise, just give me Mike, his yo-yo, and a quest to go on. I'm good. If this happened, even just on WiiWare, I would do backflips (or at least try).