There are a few moves Pokemon can only get via XD. And they put more effort into the story than most of the main Pokemon games do. Though the sequel to Colosseum, XD is superior in a lot of ways. And XD is the only way to get Lugia in the third gen without an event (of course, fourth gen has Heart Gold and Soul Silver.)
The mechanics were somewhat different (very few wild Pokemon - you steal tainted "Shadow Pokemon" from your opponents instead - and almost all double battles) as well.
And let's not forget that some of the best music in the franchise is in the Gamecube games.
Not sure what else to say, really. Anything specific you want?
Creator of Jay's Journey (see quote!) "It's not ten years old! Therefore, it sucks!" - Nostalgia whores everywhere