Twilight Princess

Garou: Mark Of The Wolves

Jedi Academy

Thunder Force V
Fire Emblem: Radiant Dawn
Yakuza 7
Contra: Shattered Soldier

Sonic Adventure 1,2 and Heroes (counting the other stories)

A Link Between Worlds - you can fight the Link from A Link to the Past as the final boss of the StreetPass arena.

Pokemon Black 2 and White 2 - Red appears in the Pokemon World Tournament as a challenger. I believe he's also in the Battle Tree in Sun and Moon but I'm not sure.

Does Stranger of Paradise count? You fight the ff1 warrior of light

Metroid Prime: Federation Force, in which you fight a brainwashed Samus

Zone of the Enders: The Second Runner
Anarchy Reigns
Splatoon 2: Octo Expansion
If "the previous game" includes prequels released decades later, Metal Gear, Metal Gear 2: Solid Snake and any old Star Wars game where you fight Darth Vader

@87th I'm saving those for "sequels where you play the villain from the previous installment"

Cool

Oh - Donkey Kong Junior

Not sure if it'd count, but in 'Rockman & Forte Mirai kara no Chousensha' you fight at the end against a bad Mega Man from another dimension/time that was corrupted after absorbing the Robot Master's powers. Corrupted by power I mean.

Azure Striker Gunvolt 2 and 3
Valkyrie Profile Covenant of the Plume
Armored Core 2
Touhou 3 and 9

I think it happens in the Disgaea's after 1 too

Who do you fight in SMT3?

@MrHoodie Raidou, the protagonist of Devil Summoner

Tales of Symphonia: Dawn of the New World

Not sure if you'd count MG1 and MG2, but since MGS3 and MGSV are prequals to MG1 and MG2 you chronologically fight the previous protagonists

@megahouten oh gotcha. Didn't that game come out after SMT3 though?

@MrHoodie You are right, it's in the Maniax Chronicle Edition that you fight Raidou, not in vanilla. Sadly, that version isn't in backloggd, but I'll update it with the HD remaster that has that fight too.
About MGS. I'm saving those for a future list "sequels where you play as the villain from the previous installment"

King's Field III

@megahouten I gotcha

Armored Core: For Answer

Mega Man Maverick Hunter X

Mega Man Zx Advent