Is megaman starforce 3 red joker better than megaman starfoce 3 black ace?

No

Well....Actually, it depends on how your battle style is, if your a full-on offensive player, then yes black ace is better than red joker, but, if your a full-on defensive player, then red-joker will be your game of choice. Either way, they are both technically the same game, except for your choice of battle styles & separate powers for black ace & red-joker noise forms that is.

Hope this helps on your decision between the 2 games, if you decide to buy one, or both if you choose. :)