You know it's funy, but Witcher 3 is an example of game where the player character is NOT the main character. Cause at the end of the day, in case most of you missed it, and it certainly looks like you did, the story of the game is NEVER about Geralt. It's about Ciri. She is the axis mundi of the plot, part Mary Sue perfect beeing with godlike powers and part McGuffin. If you think Geralt is an unstopable death machine, then what the hell is a super-powered magical beeing that can bend the laws of space and time to keep Geralt and Yenn alive after they get skewered with pitchforks,can travel through the multiverse AND is also a badass swordfighter?
Sure, the game is told from Geralt's perspective, but he never is the main character, nor the focus of the plot. Even the final boss-fight of the game, Geralt is nothing more than a side-kick, taking on the goons of the Wild Hunt, so that Ciri can go face to face with Imlerith and save the world from destruction. I find this talk of Geralt beeing a Mary Sue hilarious, becuse it obviously can only come from someone who never finished the game or understood the focus of the story ... so let me spell it out one last time: In withcer 3 you, the player, as Geralt, are NOT the main character or focus of the plot at any single point in the entire running time of the game.
But as far as games where your character is not the hero go ... well, MMOs are guilty of that alot of times, with WoW making me quit specificaly because of that. It got so hilarious that in WotLK, Arthas simply GETS BORED and wipes your entire raid of "badass" heroes with a flick of his wrist. Tirion shows up, releases the sould from frostmourne which ressurect you, and then your job becomes "be a glorified meat-shield and keep big guy busy while the hero kills him", a job that could just as easily be acomplished by an army if pesants and peons bum rushing the guy just as well as the supposed great heroed you are. Then came Cataclysm, or as I like to call it the "Let's jerk of to how awesome Thrall is" hour, and all mention of any sort of player character vanishes from the story from that point onward, with Warlords of Draenor actually going out and telling the players "you are nothing more than nameless grunts in the workings of the Aliance/Horde war machine not even worth mentionint". You are basically the grunts and footmen of Warcraft 3.
You know at least in TBC, Maiev would never have taken down Illidan without help, and it made thematic sense for her to deliver the final blow, but from Lich King onwards, the game doesn;t mince words: you are nobodies, nameless disposable meat-shields and nothing more.
I think GW 2 does a bit better, in that during the personal story of your character you become the leader of the Alliance that takes down an elder dragon and without which Destiny's Edge (they are the "main characters" of GW's lore) wouldn't have been able to do anything.