I could be full of crap here, but here are a couple of purely theoretical things I'll put on the table that I'm pretty much just pulling out of thin air:
1- All things being equal (which they very well may not be) the Gamecube disc would spin faster than the 5" disc simply because it's smaller. I mean, simply, that it takes less energy to spin a 3.5" disc than a 5" disc so it would be ultimately be possible to make a faster spinning 3.5" drive than a 5" drive. I suspect that, when other factors are included into the equation this advantage becomes moot, but I digress...
2- Also, and this seems somewhat more plausible to me, though maybe imperceptible, the Gamecube disc should, given the same amount of energy, spin up faster than either of the others.
I'm not sure why I'm even throwing those out since I lean toward neither of them making any appreciable difference, but I don't know...one thing I do know is that Metroid is, for all intents and purposes, one gigantic level. There is no (edit: intrusive) loading whatsoever, not before you get to the title screen, not between areas in the game; it is massive. It probably has more to do with extremely talented developers than the hardware, but who knows. The Soul Reaver games kind of pulled this off for the dreamcast, though not as well, and it has a 5" disc.
Whether it's the hardware or aa bunch of software coincidences, though, load times are generally (but maybe not always) lower (or non-existant) for Gamecube games, especially gamecube exclusive titles, than for their X-box or Playstation counterparts (or similar games for those platforms where Gamecube exclusive titles are being compared).
I got thinking, though, and one place where the size of the disc might prove important (or should be important if Nintendo hadn't skimped on sound hardware) is with 5.1 surround sound. Even if Nintendo had seen fit to include dolby digital hardware the 1.5gb disc might prove somewhat limiting. Pro Logic II is surprisingly robust, but it's ain't DD 5.1.
Maybe the disc capacity still would be fine, though. How many PC games have you seen that were released on more than two CD's (slightly less capacity than a GC disc)? A few adventure games or RPG's. That's just about it. I think capacity for the gamecube discs is mostly a non-issue. I really like them. I have a CD wallet for gamecube games and it's a little smaller than a fat-boy ice creame sandwhich. Kinda cool.