Yeah, games certainly aren't shorter, but in this port happy 21st century, there are quite a few minor differences between different builds. Need for Speed: Hot Pursuit 2 has to be one of the most extreme examples, EA gave an unfinished PS2 build to a different team to port it to GameCube. The result was that the GameCube version had some improvements that the port team implemented, and the PS2 team continued to add features and made some significant changes to the track designs. So what you ended up with were two significantly different games with the same name. Pretty bizarre.
So you just have to look closely at multiplatform games and the features that are important to you. I tend to play my GameCube far more than my Xbox so I'll often get the GC version even if it doesn't support digital audio or something. On the other hand, if there's a game that I think might have decent online play, I'll get the Xbox version. Most of the time though, the single player aspects aren't different enough to matter.
In any case, as the guys above expressed, I tend to play more exclusive games than multiplatform games on either system. I've got Crimson Skies, Halo, and Burnout 3 on Xbox and piles of games on GameCube. Looking at the release lists for both systems, I find plenty more GC games that I want to pick up.