Metroid: Other M
You point at a thing, you win! Okay, you point at a person, to be fair, but having the final boss of a Metroid game be a Where's Waldo segment was a bit... weird.
Mass Effect 3
Where's our big showdown with Harbinger? We had a perfectly fine template for fighting a Reaper on foot in the Rannoch mission, so why not scale that up to ridiculous size? Could even have the amount of damage you do scale directly with how big a fleet you assembled. But no. A boring, standard Marauder is the last enemy.
He lived as Marauder Shields, but died as Marauder Health. He tried to keep us from The Ending, but we ignored his pleas. Honored be his sacrifice.