Fortunately a majority of the games I have played have included protagonists that I found thoroughly enjoyable. However, as with everything in life, there have been some serious mistakes made by game developers when choosing a main protagonist for their games. What follows are a few protagonists that I think should never have been allowed to make it past the drawing board.
Lester, from Lester the Unlikely
I actually didn't even know this game existed until watching the Angry Video Game Nerd's review. Lester is indeed an unlikely hero, basically just a geeky, cowardly teenager with no heroic qualities whatsoever. Whenever he encounters an enemy, Lester will spin around and run for his life. What crowd was this game supposed to be marketed to? Nobody plays video games so they may be placed into the shoes of a sniveling coward with an embarrassing walk cycle (really, you have to see it to believe it). That would be like making a Bully game where you play as the kids who get their asses kicked by Jimmy on a daily basis.
Shaq, from Shaq Fu
Don't get me wrong, I love playing as Shaq in NBA games, but I completely disliked a Kung Fu-fighting Shaq. Maybe I'm just bitter because this game was utter garbage, with bad collision detection and impossible-to-execute combos. But a really bad design choice is that you barely notice you are playing as Shaq, it just feels like some cookie-cutter angry 7' tall guy. If the developers had even tried to incorporate some of Shaq's unique personality, Shaq Fu could have been a very funny experience and I might have been able to put up with the severe game play flaws.
The Rookie, from Halo 3: ODST
I'm probably digging myself into a deep hole by including The Rookie on this list, but hear me out first! It seems like Bungie was trying too hard to make a "Master Chief Jr." when designing this character. This game could have been Bungie's chance to introduce a completely new character with an entirely different personality and style than the no-nonsense Chief (which they sort of succeeded in with the inclusion of other playable troopers). Instead we get a completely silent character with no personality at all, who adds nothing to the Halo universe. I call him Master Chief Jr. because he looks and controls just like the Chief, but since he isn't a Spartan, we don't get any of the signature daring stunts (as well as the signature in-game respect from your fellow Marines) that make the Master Chief so awesome.
Honorable Mention: Tidus from Final Fantasy X
I ranted about this annoying brat earlier, so as a result he receives an honorable mention.