kingdom hearts 2 baby

Sonic Adventure 1, 2 and heroes all do this

oh if we're counting protagonists from other games, Lightning from Final Fantasy XIII is a boss in Final Fantasy XIII-2

the 3ds soul hackers port has both the devil summoner 1 protag and raidou as secret bosses

it's looking like previous protagonists count, so

pokemon gold/silver/crystal, heartgold/soulsilver, black 2/white 2, and sun/moon/ultra sun/ultra moon all have red as a boss fight

also the sa-x boss fight in metroid fusion is essentially just fighting samus from the previous game but that's a bit more dubious of an entry since it isn't truly samus herself though it's a near-perfect replica

on a similar note, castlevania symphony of the night as well as castlevania portrait of ruin have you fighting versions of previous protagonist richter belmont in some boss fights though he's not 100% himself in either case for differing reasons (the former has him possessed, the later has him as a ghost)

resident evil 5 has jill valentine as part of a duo boss fight (though she's being mind controlled), and resident evil 4 has jack krauser as a boss fight (who wasn't actually a playable protagonist at all until a prequel game a while later, so it's only retroactively true)

metal gear 1 and 2 have venom snake and big boss as bosses respectively, though like with krauser above they only became playable protagonists in later prequel releases

also if we want to go eeeeeeeextra dubious, star wars the force unleashed has luke skywalker as a boss fight (and i'm sure other star wars games have similar fights, like literally any one with darth vader as a boss)

Mega Man X5 does this

actually now that I think about it, pokemon ruby/sapphire/emerald, omega ruby/alpha sapphire, brilliant diamond/shining pearl, and x/y all have the protagonist you didn't pick (between male and female) as a boss

also yu-gi-oh duelists of the roses has you duel against the deuteragonist you didn't pick but i dunno if that counts (also other yu-gi-oh games typically let you duel against the main protagonist of its available anime/manga series but I don't think that really counts since you don't actively play as them)

oh yeah in the second south park game you fight the protagonist of the first game, which is literally just you in a different outfit

Dead Rising 2: Off the Record does this

Sonic Rush
Sonic ‘06
Phoenix Wright: Ace Attorney - Spirit of Justice (the first half of the final case has Apollo and Phoenix as opposing lawyers in court)
Chaos Rings
Heavy Rain

Zone of the Enders: The 2nd Runner

Anarchy Reigns

astral chain

Library of Ruina

Fun list. Here's an especially cool example of this: at the end of Streets of Rage 1's co-op campaign, if one player chooses to join Mr. X and the other refuses, both players have to fight each other.

Apart from that, you can fight Bayonetta herself in both Bayonetta 1 & 2 via their challenge modes (Angel Slayer and Witch Trials respectively). If we're counting boss fights against the protag of the previous game as well, William from Nioh 1 is a boss fight in Nioh 2.

Also, I haven't played it myself, but Transformers: Fall of Cybertron does this too. Not sure if War for Cybertron has anything similar.

fire emblem radiant dawn
Rockman EXE Operate Shooting Star
persona 5 strikers (dunno if it counts entirely)

Oh also, Jedi Academy's evil ending has you fight Kyle Katarn (the protagonist of the three previous games) as the final boss.

would viewtiful joe count?

also live a live certainly counts

havent chimed in yet but if you mean another joe, im trying to avoid 'fighting a separate entity mirroring yourself', which is kinda why i didnt include metroid fusion or something like the doppelganger in dmc3, but i understand lists like these have a lot of technicalities

Alastor/Another Joe has his own story mode

damn, forgot about that, my bad 👍

Bowser's Inside Story

Armored Core: For Answer

in god hand you can fight yourself as an optional boss, does that count

Do clones and that sort of thing count? Darksiders 2 does it like this at the very beginning