I think Sunshine has been badly underrated, but in spite of that there's really no contest here: Galaxy wins hands down. Why?
- more levels
- less collecting
- less repetition
- mind-bending gravity gameplay
The Gravity is a matter of opinion, I can see where some people will find the upside-down stuff in Galaxy really annoying. Personally, I think it's great. Really fun and challenging.
I'm really passionate about the rest though. I wasted about 20 hours searching for blue coins in Sunshine and finally gave up and used a guide. I don't actually mind collecting, but Sunshine was excessive, to say the least.
To me Super Mario Sunshine felt like it was about 3/4 done, they needed 2-3 more levels, but instead they filled it up with thousands of coins and a bunch of Shadow Mario fights.
Then there's Super Mario 64...it's a great game, very revolutionary and still holds up fairly well, but like Super Mario Bros. before it, there's just no way they're as good as Super Mario Bros. 3 / Super Mario Galaxy.