(This has probably been beaten to death by now, but I couldn't be bothered to look for any instances of it for more than two minutes.)
Ever played a video game? Being on a strictly gaming related site I'd be willing to bet at least one or two of you have. Now what's your favorite video game? Perhaps it's Mario Galaxy or Ocarina of Time, or maybe Final Fantasy VII is more of your thing. Regardless, think about the characters of that game. Who's your absolute favorite? Was Mario your favorite? Probably not. Was Cloud the main reason you plowed through FFVII? I seriously doubt it. Is Link the most intruiging character of the Zelda franchise in your opinion? The answer's obvious. The side characters are most likely much higher on your list, such as Tifa or Luigi.
Why is this the case? Well the most obvious reason I can think of is that the protagonist is, nameless or not, supposed to represent the player. His (Or her's, though admittedly the majority of video game protagonists are male.) actions are that of your own, and you control nearly every decision he makes. Therefore the developer tends to create an overall dull hero with an admirable goal that no one could possibly have qualms with, such as saving the world.
This leads into my other reason for the massive percentage of uninteresting protagonists. Take Persona 4 as an example, Chie and Naoto, two of the most widely loved secondary protagonists/waifus on the site, are each beloved for their rich history and developed personalities. If you enjoy the characters, you're obviously going to have an overall superior experience with the game, so why not make one of them the main protagonist? Aside from the obvious point that you'd lose the element of the protagonist essentially being your own blank canvas, consider that you didn't like these characters, or just found them to be 'alright'. (I'm in the latter boat.) That would greatly diminish your enjoyment of the game as a whole, seeing as you wouldn't even agree with the goal or choices of the person you're forced to play through as. The generic mascot works as while nearly no one loves them, no one hates them either.
Is there potential to have protagonists with depth? Obviously, yeah. There's already games that do it. Pretty sure Last Of Us does, and everyone seems to love that game. (I really should get around to actually playing it, it's still sitting on my shelf.) Some other examples I'd actually know about exist too! "Hell Yeah! Wrath of the Dead Rabbit" is a brutal comedic platformer by Akedo Studio and published by Sega, it features Ash, the douchebag skeletal rabbit prince, who kills people for posting suggestive images of him and his secret lover, a rubber duckie. His character isn't exactly deep, but he's certainly more fleshed out than the rest of the characters, and while he's very vocal on his unfavorable opinions, he's a good laugh, and a fresh twist on the same-old recycled platformer mascots. Another great protagonist is Cthulhu from the appropriatley named Cthulhu Saves The World, an enjoyable little indie RPG by studio Zeboyd Games. Once again, the mascot protagonist isn't exactly your ideal hero, in fact the only reason he's saving it is so he can lift a curse allowing him to once again destroy it again. He's undeniably a hard character to like idealogically, but once you start playing you grow attached to his nonsensical beliefs and strategies. Neither game is a masterpiece, but I still recommend looking into both of them.
Overall, I guess the moral of the story is to try new things. Er, stick to your gut. Yeah, something like that. I can sense you judging me already. Regardless, give me some feedback, this was my first C-Blog after all.