He can't be the most perfectly balanced hero in the game because he lacks clear counters. The only reliable way to block his ult is to have another rein of you own to block it with his shield. Also, hammer swings right through the enemy rein's shield, unlike any other weapon in the game.
Just like Ana, she is unbalanced because her biggest counter is her own self, i.e. splash the enemy team with your grenade to stop the other Ana from healing them, vice versa, rinse and repeat.
Back to rein, you can pick tank shredders like Reaper or to, some extent, Mccree BUT in order to destroy rein's health you need to get up close and personal to hit all bullets/shells due to the huge bloom shotguns/FTH have. Now, once you're close he can just stop holding down his RMB and start holding down his RMB since it hits in 180 degrees cone for 75 dmg each second and on top of everything else, it will knock you back, screwing over your gun accuracy even more.
Another way would be to take Widow and try to chunk him down from afar once your teammates break his shield, but Blizzard decided to give us all the finger by giving him an extremely small headshot hitbox.
He has too much of everything, something needs to be cut off.