I really hate to say this and as much as this is going to make me sound like a smartass I must say that no Master Hand and Crazy Hand are not apart of the Mario series.

Question:
Did Hal Laboritories create the Super Smash Bros. and Super Smash Bros. Melee games?

Answer:
Yes they did.

Question: Who creates the Kirby games?

Answer:
Why Hal Laboritories does.

Assumption:
But Mario appears in Super Smash Bros. Melee and he is in there with Master Hand and Crazy Hand.

Answer to Assumption:
And so is characters from Star Fox, Metroid, Fire Emblem, Legend of Zelda, F-Zero, Pokemon, Ice Climbers, Earthbound, Kirby, and Donkey Kong.

Question:
So does this mean that these other characters are also relative to Master Hand and Crazy Hand?

Answer:
If you assume that Mario is, then my suggestion is that the others must be as well.

Back to the subject at hand though I still think that Mario & Luigi should take this. They are going to be working as a team, while the others are clearly working against each other. Really anything could happen, but I just see the Mario Bros. being able to subdue their opponents with their cohessive teamwork.