64 and Thousand Year Door tie for me. I definitely prefer the worlds of the first one a bit more, but I got more into the story in the second game (also, Glitzville was pretty much the greatest place ever). And I agree with the original poster, please bring back the buddy system, Nintendo! Honestly, I was okay with the last two entries in the series even if I didn't like them as much, but more interaction from partners has always been part of what made the first two games so colorful, at least to me.
Hmm







