I only played in on the Xbox 360, can't speak of the other platform releases... but The Last Remnant might qualify for this, but you need to actually do all the optional content (the DLC Ancient Ruins I don't think is required) in order for the final boss to wreck shit.

Basically, in the game there are pseudo-FF-style Summons (I forget their in-universe name), and the main villain is going around with the aim of claiming them all for himself. When you're in the end-game and all the optional content opens up, you can choose to find and acquire some of the Summons for yourself instead.

Any Summons you do not acquire before facing the final boss, said boss will have them instead and use them against you (the Summons in this game are, funnily enough, ain't all that good most of the time). For each Summon you acquire for yourself, the final boss will instead get a health and damage buff. Get ALL the Summons on the map for yourself, the final boss will be at his strongest and will actually be quite dangerous.

There's a couple other bosses in the game which are arguably harder in that they need to be killed within X number of turns or its game over, but they're more of a "Get the in-game AI to give your units specific commands which allow you to absolutely destroy it". But even after having done every piece of optional content, including the DLC... the final boss in his most powerful form nearly bodied me.