What most of you can apparently agree on is that a protagonist should not be someone you'd find off-putting in real life (e.g. male: loser and pervert) and should have some flaws....in other words, a distinctive personality.
What hasn't been answered, however, is: how different is too different? (Unless it has, in which case I apologize and ask politely for a link)
What about a female lead that is, for all intents and purposes, a tomboy and does not miraculously change into a lady by the end of the game? (And I don't mean the cute kind of tomboy you find in animes, but the tough, one-of-the-guys kind)
Or a protagonist that smokes/ has bad habits in general? (Smoking is bad, children! Don't do it!
A protagonist that tends to be an asshole and solves conflicts by hitting rather than talking? (No matter if they have a reason for it or not...)
And what if that person is female?
So yeah, what would make you go "Nah...where's my generic, run-of-the-mill mary-sue/gary-stue protagonist"?