I get what you're saying, i think part of it is just the way it has to be tell a compelling story. It'd be a short movie if the hero just instantly won everytime. To the Batman vs Superman example though, in the comics, Doomsday is basically engineered to kill Superman. If there was ever a being that should be able to kill him, that's the one. (which is why DC wasting that story so soon was so stupid) Another Kryptonian can match his power, and Doomsday is basically a Kryptonian monster. I think another layer to be considered is that the good guys don't try to win at all costs. They generally all have a 'no kill' policy. So they don't tend to fight at full strength. They also have to be mindful of innocent bystanders. The bad guys don't care who they hurt, and they want to kill.