I'm surprised this hasn't been mentioned yet: Melee was a much more dramatic upgrade, released after a much shorter waiting period. Melee came out just over two years after 64, had beautiful graphics, added several fundamentally new game modes, and more than doubled the size of the roster. Brawl came out almost seven years after Melee, marginally improved the graphics, grew the roster by less than ten slots, and was basically just a more polished version of Melee. Whereas Melee was the definitive upgrade to 64, there's no major reasons to upgrade from Melee to Brawl.
I stand by my Windows analogy. 64 was Windows 98: a bit ugly and buggy, but worked well enough. Melee was XP: significant upgrades in usability and stability, and dramatically better-looking. Brawl was Vista: took seven years to come out, after innumerable delays and huge amounts of hype, and didn't make any major changes, yet still cost as much as the last one.
Also, we weren't expecting to know all the exciting stuff about Brawl months before it was released. Pretty much all the interesting new characters were revealed on the site long beforehand, and most of the unlockable characters in the game were veterans.
But my biggest pet peeve with the game (aside from the trophies) is how obvious it is that Sonic was a last-minute addition. There's no excuse for that. Sakurai and Sega should have been sitting down with each other from the day development started. It shouldn't have taken until the summer of 2007 for one side or the other to go "Hey, as long as we're putting third-party characters in there, how about Sonic?"