Order doesn't matter in survival, in survival it takes all your total stats and gives 1/4 to each ninja. Thing is most good players focus stats to min/max, best refines on your move 1 & 2 ninjas, best defensive magatams on your tanks and etc. And the way survival works ruins that.
The problem is gear for enemy works perfectly fine, which is dumb, its should be same for both team. Either both use 1/4 total stats or both use correct gear.