Diablo 2 - previous game's protagonist is a host for Diablo now

Oh, shameful I didn't think of it straight away - Kyle Katarn is the final boss of the darkside path in Jedi Academy!

as a jedihead i am similarly ashamed

We have also both forgotten that he's the final boss of Mysteries of the Sith as well.

nobody ever beat that game

Dawn of Sorrow counts on Julius mode.
Can also throw in FFXIV Shadowbringers since you fight the Warrior of Light from FFI.
Mega Man Zero 3 is a weird example since you're fighting yourself from a past game but it works.
With weird timeline shenanigans, both Virtue's Last Reward and Zero Time Dilemma count.

Richard Miller is the final boss in Time Crisis 2's Crisis Mission mode. https://www.youtube.com/watch?v=_XPFKGpUl7M
Resident Evil has played up this dynamic a few times, particularly in pre-release trailers, though it's debatable whether they've ever really delivered on it (Evil Jill in 5, Chris vs Leon in 6, Mysterious Chris in 8).

Armored Core: For Answer has you fight a hero from Armored Core 4.

Also Mario and Luigi: Dream Team has you fight Bowser who was a hero in Bowser's Inside Story.

Castlevania: Curse of Darkness
Drakengard 2
Digital Devil Saga
Disgaea 2

Probably a stretch, but when you die in ZombiU the game sets you up as a new survivor, after which you can find your previous character as a zombie and fight them to get your stuff back

Castlevania: Portrait of Ruin has a boss fight against the memory of Richter Belmont, if that counts
Contra: Shattered Soldier has Lance Bean as one of the main antagonists
Will you accept Bionic Commando 2009

As anyone who has been following me on Backloggd for a while will know, I will accept pretty much any example

King's Field 3 - the penultimate boss is the protagonist from King's Field 1!