What gets me the most is how people are complaining how there weren't more third party characters in this game when it should be obvious to anyone that Sonic and Snake are the third party representatives precisely because they were the easiest to negotiate. Kojima actually asked Nintendo to put Snake in, rather than the other way around, and while Konami certainly had to sign off on the deal it's highly unlikely they'd want to displease the creator and mastermind of their most critically acclaimed and financially successful game franchise. Sega and Nintendo already had some kind of deal worked out for licensing of each other's characters due to that asinine Sonic and Mario Olympics game, and considering Sega has finally seemed to realize that Sonic is teetering on the pit of complete irrelevance I'm sure they were more than happy to allow him into what is one of Nintendo's most successful game series.
And it should have been clear from the start that the number of third-party characters in the game would be small because the more companies get involved, the more of the profits Nintendo has to give up, and considering Melee was the best-selling game on the Gamecube I'm sure they weren't particularly thrilled at the prospect of having to hand a lot of the money they would make of the sequel away to other companies.
In short, kids on the Internet are stupid.