This got me thinking about what protagonists I've actually liked, and made me realize... barely any, and even then, usually not because they're well-developed, because the vast majority of game writers (possibly all of them) suck. So I'm left with a bunch of brainless beefcakes and Mario. I'm gonna side with Mario every time.
Some of my favorite protagonists so far have been the universal "Everyman" type of character, like Mario. He's just a fat dumb plumber who gets sucked into wacky adventures, and doesn't need a chainsaw, a gun, a cigar, a six-pack, and a devil-may-care attitude to do it. It could've been me! Same goes for Jade from Beyond Good and Evil. She's a photographer who works at an orphanage and then gets sucked into wacky adventures, and doesn't need long blonde hair, giant tits, and a gun for an arm to do it. Other "Everyman" characters it's easy to identify with are Gordon Freeman and the guy from Out of this World, and sometimes the voiceless nobody like Crono or Chell works too. They all kick ass without bionic implants and/or insane training to do so (Samus, Master Chief, Mega Man, everybody, etc.).
For characters I can't identify with but like due to their personality, Wario was cool since his motivation was always greed and you just steal gold. I liked Abe from the first Oddworld. I never played the sequels, but he was cool in the first one. I like Donkey Kong 'cuz he wears a tie. Any time I had a guy named Wolfgang in X-COM he became my favorite guy in the squad and I'd give him the best weapons and armor and protect him until he got promoted to the top.
Can't think of any other protagonists that weren't boring as hell. I liked Terra/Tina from FF6, but I don't know if you can call her the protagonist. It's more of an ensemble cast not starring any particular character.
Man protagonists suck.