He needs to do that in order to keep balance and make the Manga interesting, lets take a Look at Pain when he was introduced in the show as a God, everyone was so exited to see that what he can do, a person who leads an organization full of powerful Shinobi,
and when we saw him invading and destroying konoha, it gave us chills and curiosity as to how Naruto is gonna take this man on, had Kishi not made him so op could we enjoy that chapter.
would you like to see side characters like Shino,TenTen,Ino, etc fighting on the equal grounds with a guy who is suppose to lead one of the toughest groups in the manga.
Same thing applies here, if Madara,Tobi are not so op then we won't have any curiosity or excitement.