Mario galaxy also has something like this

Oblivion Shivering Isles dlc has a fight against shadow protag
Tomb Raider Underworld has a Dark Laura that seeks out to ruin her life (Also Tomb Raider: Anniversary)
Alan Wake American Nightmare has Mr. Scratch (Dark version of Wake)
Styx: Master of Shadow has you going against yourself, but I don't really think either version are "Darker" than the other sooo
Bloodstained: Ritual of the Night has a mimic Boss
Metroid Fusion has Samus's suit being controlled too
If you are including Crunch from Crash, then probably Metal Sonic AND Shadow the Hedgehog would surely count (all of them are MADE to counteract the protag).
Scribblenauts has a evil Maxwell
Minecraft cause of Herobrine 🤭

@moschidae @Snigglegros Awesome! Obviously this list is kind of limited to my knowledge so thanks for those suggestions I'll add them!

@Snigglegros I thought about the Shadow/Metal Sonic stuff and I don't know if I have the resources/experience to figure out every game they're from so I think I'm going to eliminate Crunch from the list to keep this list more of a "dark shadow versions of the protag" instead of just foils to the protagonists like Crunch, Shadow, and Metal Sonic are.

yeah cause I figured you didn't want Vergil type characters, but I could see Crunch/Metal/Shadow as different theoretically. Maybe shadow is more vergil, but Crunch and Metal maybe??? I think they were both created by their respective mad scientist as a "clone" to defeat the protag. Crunch is pretty different than Crash tbh, but maybe Metal could be an actual dark version of Sonic? IDK, Just wanted to share my thought process on them.

Prince of Persia Two Thrones there is the "Dark Prince" if I remember right?

Streets of Rage also has Mona and Lisa, evil versions of Blaze if that counts?

@FallenGrace Added! Thanks!

would lynx count? from chrono cross. he's not an evil serge clone, but, well...

id from xenogears. same deal, though.

@zn0 Thanks for the comment! I really like both suggestions, but I decided to focus on "dark" or "shadow" versions of the protagonist rather than characters that are just really good foils to the protagonist. I love Lynx though. Haven't played Xenogears yet but I'll look up Id and see if they might count!

Persona 5 strikers

chrono cross probably doesn't count — a body swap is something else, really. but id is... well, i do i say this without heavily spoiling things? he's not exactly a shadow, or an evil clone or copy of the protagonist, but you might find it interesting nonetheless.

@NOWITSREYNTIME17 Good catch! Totally forgot the boss in Kyoto! Thanks!

@zn0 I tried to not read too much into it to avoid being spoiled but it definitely sounds cool so far.

Not sure if this counts, but you get to fight shadow versions of almost every playable character as part of the Great Maze in Super Smash Bros Brawl. There's also a mission where you have to fight Shadow Link as Link.

Cosmic Clones are also present in Super Mario Galaxy 2 by the way.

Ninja Gaiden Black has the Ryu Doppelganger!

In the F-Zero franchise, specicfically F-Zero X, Blood Falcon appears, who is, quite literally, a evil clone of Captain Falcon, and I think it counts. Plus, in Kirby and the Amazing Mirror, Shadow Kirby appears, and while it's not an ''evil'' version, it is a counter-part to the original Kirby.

Just two examples that come to mind and I belive could fit, but I'm sure there are even more. Great list!

@Drax @gruel @DeemonAndGames
Great suggestions! Thank you so much I've added them all :)

KOF 2002; Kusanagi

@Reddish @Lag0n Nice! Thank you

Doppelganger boss in Megaman 1 and its remake Megaman Powered Up
Doppelganger boss in Megaman 3
Quiet from Gameboy Megaman 2 is an evil brainwashed version of Megaman from an alternate future
Doppelganger boss in Castlevania 3
Doppelganger boss in Castlevania Chronicles
Doppelganger bosses in Castlevania: Symphony of the Night
Doppelganger boss in Castlevania: Portrait of Ruin
 Doppelganger boss in Castlevania Lament of Innocence
Evil clone mirror match in Sonic the Fighters
Shadow Doppelganger in Double Dragon 2
Evil Version of Postal Dude at the end of Postal Brain Damage
Your best friend in Dark Seed 2 is technically your Dark World counterpart

Shadow Link appears in Link Between Worlds, Tri-Force Heroes, and Link's Awakening 2019.

Mario's Cosmic Clones also appear in Super Mario 3D Land.

YMMV on if Metal Sonic should count or not. If so, these games he has an active role in: Sonic CD, Sonic Triple Trouble, Knuckles' Chaotix, Sonic Heroes, Sonic Rivals 1 and 2, Sonic Generations (console/PC), Sonic 4 Episode II, and I think there's more, but those are his major appearances.

Mecha Sonic appears in Sonic 2 and Sonic & Knuckles. There's also Shadow the Hedgehog but he's more of a parallel to Sonic rather than a "dark" alternative.

Kingdom Hearts 2.8, also technically Birth by Sleep has Vanitus and Ventus
In Shin Megami Tensei: Strange Journey there's an enemy called doppelganger which is just a shadow version of the protagonists as a portrait
Persona 4 Arena Ultimax has shadow versions of characters.
Persona 2 has shadows
Mario Wonder has shadows similar to galaxy
Rayman
Arguably the Fate series has "Alter" versions which are corrupted versions of summons but the protag isn't the summon
Silent Hill 3

The following two are spoilers:
Spider-Man Edge of Time
Tales of Bersaria

Hollow knight, you fight your shade everytime you die to pick up your geo and part of the soul meter back.

Omega, from Mega Man Zero 3

Shin Megami Tensei: Strange Journey (the Doppleganger demon is identical to the protagonist, and it's the only SMT where this happens)

Whould Bayonetta count since Jeanne is pretty much the same character with same moveset?

Fate/Samurai Remnant has the protagonist fight against a shadowy version of himself to master a new form of swordplay

Wow I didn't expect to get so many suggestions all at once! Let me try to address them all.

@MrHoodie Thanks for the suggestions especially for Megaman and Castlevania! Looks like they have a habit of this. I debated Jack from Dark Seed 2 at first since I didn't think a dark version could simultaneously be friends with the protag, but I read the ending and decided he deserves a spot.

@electrode Thanks for the dark/shadow Links I missed. I mentioned in a previous comment that I'm not counting Shadow or Metal Sonic since they are more of foils to Sonic rather than "a dark version of him"

@bitterbatterdog I really don't like Ven and Vanitas but I think they do fit so I'll begrudgingly add them. Also I mentioned on the P4A entry that Ultimax has them two but I don't feel like it deserves another entry. I won't count the alter summons for the reason you mentioned but they do sound pretty cool. Also I tried to look up the ones you mentioned for Spider Man and Bersaria and couldn't find anything that made sense. Could you post an explanation or link? Thanks!

@maradona Shade counts for sure thanks!

@Lag0n I don't think I'll count Omega for the same reasons I'm not counting Metal Sonic, Crunch, etc

@Aziamuth That Doppelganger demon sounds awesome I need to play that one! Thanks!

@RoyalFury I don't think I'll count Jeanne since she isn't Bayonetta she's a separate character who just happens to play the same as her. Appreciate the suggestion though!

@01156 That's pretty close but from what I can tell this is more of a mechanic to help you with learning the techniques and isn't an "evil version of the protagonist" as far as lore goes but I could be wrong.

Feel free to debate or post resources for anything that I've rejected for now!

This list was mentioned on the Discord server since something similar came up 👀