Megaman X
He wouldn´t simply be a Samus clone, he could use different attacks from the most famous bosses he defeated back in the days.
Megaman Zero
Of course, he would excessively use his Z-Saber, but he has got other weapons too (Buster, Shield Boomerang, Triple Rod).
Banjo and Kazooie
Oh god yes! Please!
Both of them could use the whole lot of moves they learned in their previous games. They could even seperate in Battle and fight like the Ice Climbers with one exception: You can choose if you want to play as Banjo or Kazooie, the other character would follow you.
Geno
The special techniques he learned in SMRPG would probably kick ass (Geno Whirl = FATALITY!)