Probably covered but:
The main villain is so strong that no one but the main protagonist can even touch them. Off the top of my head the Shishio fight in Kenshin was really bad at this. Sano's double layer physics-breaking punch did literally nothing to Shishio..DBZ got pretty bad about this at times too, but Bleach takes the cake for me when all the captains working together couldn't even scratch Aizen..
It's fine to have your main character be the strongest, but when you have a large cast of heroes the worst thing to do is make them all useless, have them contribute, even if only in a small way. Strawhats vs Oars and the final fight from FMA especially are good examples of how to have everyone pitch in.
/rant