How To Defeat The Main Bosses:

Mach Jentra:-After you find Axl in the maze and then a cutscene will come showing Zero .Then find your way in the factory till you reach like a big door .The best team to fight him is Zero, X & Axl from the beginning. put all in hyper mode and if possible use Axl's main move and turn him into Silver Horn.If any body is near death change them to Massimo & Spider .Use their main moves but don't destroy his minions..he'll just call more.
try to protect Axl & Spider cause they can hit enemies in air or on the ground.If & only if he is on the ground use Zero's and X's main moves(in hyper mode)

Wild Jango:- This is easy because you get Spider and you'll have Massimo,X and Marino.Put Spider,Massimo,X in the team and keep attking him with main moves and fire moves.