I don't think Galaxy made people point out flaws from 64. If anything that happened with Sunshine, or even before. We all knew that Mario 64 wasn't perfect by any means, but I think two things come into play here.
1) Nostalgia. It was the first 64 game (and 3D Mario) all of us played and I'll never forget the way it completely swept me off my feet.
2) The accomplishment of the game at the time. The first ever fully 3D game controlled by the analogue stick.. and yet it was executed so damn well that it still holds up today. I still have no idea how Miyamoto pulled it off.
So while Galaxy is definitely more technically sound and polished than 64, it's nowhere near as groundbreaking or fresh. And I think that's what Mario 64 will be remembered for.
On a side note, this is one of the reasons the Mario platformer series is my favourite. Nearly every game is a timeless classic in the true sense of the word. The graphics, gameplay and presentation of, say, SMB3 can still be appreciated as gaming excellence so many years after it has been released. To me, that's the mark of a generational game. It's similar to movies - somehow 2001: A Space Odyssey has aged incredibly and would be considered amazing by today's standards.