What I've posted in the tags are major spoilers for around the end of the game, and probably the reason SSB:B would get spoiled by the inclusion of Mother 3.
I know what they mean, I think. They're talking about Claus. Very late in the game, he gets a whole lot of powers and abilities. He's not very strong for most of it, and Lucas is. At the end, the major spoilers is that he ends up having all the amazing abilities. If he winds up as a fighter in Brawl, he'll have those abilities, and the game will be heavily spoiled.
Edit: I don't think it's the tragic spoiler, because from what I've read, that happens early in the game. I personally, have tried to find out info on the game, but without spoilers, but have failed in some respects of this. The only real spoiler I know is the one I posted, but it seems to me like that's the one they would be worried about.
Covert editing tag!