Think of a surprise end to a story, where the good and evil battles over a weapon, that can destroy all humanity. They just give them too much power, so the combat lacks tension as they are invincible no matter what. I haven't seen most of the new superpeople movies just for the reason you state. Take away expensive effects and the movies will be unwatchable.

My suggestion to fix it would be just to give them far less power. Have seen Divergent for example? There are people clearly stronger than others, but they are still very vulnerable, so the government shooting them actually makes sense. This is what I would like these crazy movies to be. Give them weakness, so tension and dozens of plot twists come on scene.