Tough question for me personally. I have strong nostalgic feelings for both of these games, so I guess that aspect kinda falls flat.
Really loved the water mechanics in Mario Sunshine. Its addition really made the game feel unique (compared to Mario 64) and it's also put to good use. Another aspect I loved about Sunshine is the tropical setting. Really gets me into the mood of vacation, though the world can be limited due to its relatively small size and similar look.
Now a quick look over to SM64. Ah yes... that first time playing with my brother, screaming: Oh my gawd, you can move around freely in all directions! And that's the reason I choose SM64 over Sunshine. Both games are some of the best in their respective genre, but SM64 had that 'WOW' effect going for it.
All in all i prefer SM64 over Sunshine. I mean, can you say no to this soundtrack? http://www.youtube.com/watch?v=uqcPSbkS9TQ
Lyrics: He He He He Ha Ha Ha!
