Manaphy is incredibly strong and destroys stall you are right. But it is not impossible to beat. Manaphy is no godly fast. Fast physical and spatker can weaken manaphy into manageable. Also, manaphy needs health preservation. Sadly the teams manaphy beat are mainly defensive. Banded weavile, gengar, alakazam and other come in a shred manaphy if it is speed and spatk invested. There is also unaware clefable and combined with chansey can out stall it. Another option is haze milotic, or roar/whirlwind. Finally klefki can be used to seriously hinder its performance. Checks are out there, you just arent using the right ones. A check in not always defensive, sometimes you much look at revenge killers