While I agree that not having guest characters return should be expected, I think its a little different with smash bros.
Yes, Snake only got in because Kojima asked Sakurai to include Snake. Yes, it could be that it was only for one game, but nobody really knows that for sure. These two are apparently close friends, so if Kojima wanted Snake in for that reason, I don't see why Snake HAS to be removed, just because he is a 3rd party character.
Sonic is a wee bit different. He was the most popular character going into Brawl, and if he were to be removed, the backlash would assumably be worse than that of Mewtwo's removal. Meanwhile, Sonic hasn't had much success lately, so for Sega, it may be a good idea to continue their support of him being in the game.
Sure, you can argue that it is a business, and companies aren't going to let people use their characters all the time, but this situation isn't exactly black and white, more like a gray area. Especially, not that it matters, but Sakurai has mentioned and acknowledged that Sonic and Snake were well received by the fans. Whether that means anything for those two characters, i'm not sure.
Also, compare SSB to PSASBR. The latter has I think 4 3rd party characters on the roster, mostly for promotional reasons. Is it possible that those characters will stay? Absolutely. Hence why I don't think Snake and Sonic are so sure to be cut.
Like I said, business such as this can be a two way street and a very gray area. But I do see both sides to the debate. We will have to wait and see I suppose.