Generally, I agree with the basic premise here that a lot of Nintendo's Gamecube sequels aren't quite as great as their N64 predecessors. However, for these three in specific, I have mixed opinions:
Wave Race - Yeah, the N64 game is better. The N64 original is really incredible, the best water racing game ever! I do quite like Blue Storm (GC) as well, but it's really hard and less fun than the original.
F-Zero - F-Zero (SNES), F-Zero X, and F-Zero GX are all among my favorite racing games ever. I love all three of them so much, it's way too hard to choose between them... so I don't. It's a three way tie.

If I HAD to choose one it'd be the N64 game, probably, but GX is areally amazing game, and so is the SNES original.
1080 - Here I'm going to disagree with the usual position -- I like 1080 Avalanche (GC) more than the original N64 game, actually. The N64 game is a bit more simmish, I like the slightly more arcadey Gamecube game... 1080 for the N64 is certainly one of the best snowboarding games of the 5th generation, but I do like Avalanche more.
For some other GC v. N64 comparisons of games published by Nintendo, as I said earlier, the N64 wins most of them, including Wave Race (above). OoT is better than the GC Zeldas; Twilight Princess is second on my list, the others behind. Mario Kart 64 is better than Double Dash (GC) by a wide margin. Mario's Tennis (N64) is better than Mario's Power Tennis (GC). Mario 64 is better than Mario Sunshine. Star Fox 64 is of course better than either Gamecube Star Fox game by miles. Paper Mario (N64) is better than Paper Mario: The Thousand Year Door. And Donkey Kong 64 is better than Jungle Beat, for sure (forget the haters, DK64 is amazing!).
And then there's F-Zero, where I probably would lean slightly towards the N64 game, but love the GC game just about as much.
The GC does win a couple, though -- in addition to 1080, SSB Melee is better than SSB (N64), and Custom Robo: Battle Revolution (GC) is better than the two N64 Custom Robo games. That's not only because the GC one got a US release and the N64 games didn't, though; the N64 games actually play just as well as the GC one, but only the GC game has four player battles -- the N64 games are two player only. For that alone, I give the GC one the edge. The Custom Robo series is fantastic though, such under-rated games! It should come back.