Which version is better?

Generally Gamecube and PC, PS2 is a bit slower and Saturn is a completely other game. Gamecube is more wide spread, you can play on an emulator too. While PC is a bit harder setup. ( btw pc > gcn ;D )

Which is better for runs?

Mainly just preference, Gamecube and PC have different handling so use whichever you prefer.

So GameCube and PC are better versions? I don't know

Yeah there the best versions overall, but I wouldn't say one is better than the other

So I need to chose

Keep in mind you can use a controller more comfortable on your hands for PC, while you are kinda stuck with the GC controller for GC, obviously. Those trigger buttons kill my hands after awhile.

PC is what I prefer to run it on just for ease of recording and streaming