SMB3 was a revolution. SMW was an evolution.

I personally prefer SMB3 because the controls feel tighter, where SMW sometimes feels "floaty". But it's a subtle difference. SMW gives you way more content, but not all of it is as good or as well-designed as the levels from SMB3 (though again, the difference is subtle.)

They are both all-time top games, as is Mario 64.