The Thousand-Year Door had just about the best plot in a Mario game ever. Serious as it was, 'twas still awesome. There's no possible way for a Mario game to be 100% serious, though. It's gonna have comic relief, inevitably.
One thing I've been thinking over... the only games that really feature THE Yoshi, that one, green Yoshi, are the spin-offs... that is, when it's sure that it's him. SMRPG and SM64DS are two exceptions. All other times, though, it's like, "You're a green Yoshi, but you're no different from the rest of the Yoshis in the game, so we can't really be sure." Which I find lame. Toad is in the same position, though I suppose there were really seven of THE Toads to begin with. All I'm trying to say here is, there should be a game in which Yoshi and Toad are distinguished from the rest of the Yoshis and Toads.