I'm somewhat glad a new F-Zero didn't come out on Wii, despite the controller perhaps being one of the appealing aspects to bring it out for it. I can still imagine a GC controller would have been compatible, and motion controls inferior, like MKWii.
F-Zero is sort of like the Smash Bros games in that one a generation is probably the best way for it. GX was graphically one of the best GC games, and a Wii game would have just been on the same level as it. So apart from motion controls (which would probably be optional), it would have needed a lot more added to it to make it special.
It's definitely the best way to wait till Wii U for the next instalment, since HD will do it the justice it deserves, as well as provide us with, hopefully, the full 30 players online races that it desperately needs. Wii couldn't provide that, so I think it would have been a slightly pointless entry after GX if it came out on Wii. At least with Wii U it can give us HD, online and motion controls, and hopefully more.
I personally thought GX was the best entry. Crammed full of content and a quality machine customisation feature. That's another thing the Wii U controller could provide - the ability to draw high quality images to stick on the ship. Imagine just spinning your machine around on the tablet, zooming in and spraying it. There's so much potential for F-Zero on Wii U.