Well, the ability for Pit to use two different decks does give him an advantage, but I think that the differences between the decks will balance it out in the long run. If you choose to attack opponents from up close in order to deal more damage with the red deck, you risk having to use the lesser defense of it if the opponent counterattacks. On the other hand, if you choose to attack from range, your defensive numbers increase, but you are unable to deal as much damage.

As for the Final Smash, the fact that the opponent knows the attack power of the Centurions does give them an advantage when defending, but even if they do completely defend against the attack, they now have one last defense card to use against Pit and his ally later on in the game. Eventually, the opponent will have to discard 5 cards in order to get rid of all of the Centurions, so even if they prevent all of the damage the Final Smash will still have a significant effect.