I imagine my top three would be

Mario
Link
Lara Croft

Yoshimitsu
Chris Redfield
Jill Valentine
Tidus
Cloud
Marisa
Reimu
The'elder Strolls (my FF14 character lol)
Teruyo (my Where Winds Meet waifu)

Ive well over 1k hours in MHW/Iceborne so i guess my hunter is my most played character in a single game

Tho if you combine games, its probably Link

The player character of Wing Commander 1&2 is supposedly same as "Maverick" Blair in 3&4, so that being my favorite series makes him likely.

Monkey Island being another favorite, Guybrush Threepwood is high. But despite replaying at least one MI almost every year, that may not make huge hours.

Other than that there's no obvious option, as I haven't played that much Marios, Sonics or Zeldas.
Of those Sonic would be top one, but I don't expect to get in my top 3. But Sonic may win by standard of "character in most games I've tried at least once" (largely due Sonic Gems collection on PS2 - and my general emulation history).

Anakin Skywalker/Darth Vader is likely in my top 5 - at least in number of games if not hours - with LEGO Star Wars games, Episode 1 Racer (two versions) and Battlefront II.

I have played at least three Spider-Man games, plus him in Marvel vs Capcom series.

Then there's Indiana Jones, with the old Lucas adventures, Infernal Machine and LEGO.

In hours, makes me wonder if I've played so much Civilization or other historical strategy games that some historical person could win? Caesar, perhaps?

And having played lots of driving games, maybe some classic car might be my most played "character", like Dodge Viper. Or due numerous rally games, Lancia Stratos or Delta, Toyota Celica or Subaru Impreza.

Edit: I completely spaced on Sea of Thieves!

I love this question!

I did some quick, unreliable math...

1. Myself, if that counts – 800+ hours (all from Animal Crossing)
2. Link, in all his forms – 750+ hours
3. Mario – 500+ hours
4. My pirate from Sea of Thieves – 400+ hours
5. Dr. Mario – 400+ hours (almost all from Super Smash Bros. Melee)
6. Bowser Jr. & Koopa Paratroopa – 400+ hours (all from Mario Kart: Double Dash)
7. Samus Aran – 250+ hours
8. Baby Rosalina – 200+ hours (almost all from Mario Kart 8 Deluxe)
9. Lara Croft – 200+ hours

Probably Kratos.

There's only so much Mario Party a man can play...

Definitely Mario. While I have played a ton of Zelda BotW/TotK, I haven’t played many Zelda games. Meanwhile, I’ve 100% completed every mainline 3D (and almost all 2D) Mario games multiple times AND have even 100% some Mario ROM hacks (e.g. Mario 64: Star Road, getting around to SMSunshine: Eclipse). Plus, my playtime of Mario Odyssey alone is only a dozen hours below my playtime with BotW (235hr v 247hr).

I actually have no clue.

Genshin Impact is by far the game I've spent the most time on in my life, with 2500+ hours, but I've always been changing characters to play with. If we consider the protagonist, Lumine in my case, is the character I'm always playing with in the story and events, then it's she by a very long shot, but if we are considering the actual gameplay, I really have no clue.

If I spent 1 year with a character on my main exploration and combat team it's around 600 hours playing with it.
Maybe Bennett? Still is a support on some of my teams after all these years, even as he rarely is in my exploration team, which takes a lot of time, for a long time now. But its hard to say.

Hoshimi Miyabi from Zenless Zone Zero is in my farm team and in one of my 2 or 3 teams for all combat content modes, so easily more than 600 hours with her there as well.

The protagonist from Pokémon Violet, as I have 650 hours there, if we consider than he is the only managing the pokemon in the battles.
How many times have I played Pokémon Crystal tho? Who knows lol.

The character I've been playing with for the longest time, considering how young I was when I first played it and it still has games coming that I play, is Sonic the Hedgehog, but definitely not the most time spent playing with.

Most played for sure is my main car in Rocket League (Jackal).
Second most likely Link.
Third probably Mario.
I have played a ton of Borderlands throughout the years, but characters change from game to game there, so no individual character from that franchise could crack the top 3. My Sea of Thieves pirate also has hundreds of hours of playtime, but I think since Link and Mario are in so many games all the way back to my childhood, they must have amassed more overall playtime.