No offense but it's sad to see almost nothing but non-characters on this list. I'd have to vote for Joel because he has abundant character flaws and he actually develops a bit over the course of his journey.
That's my problem with picking any of the major Nintendo characters; very few of them are developed in any significant way that isn't terrible. Wind Waker Link is one I could possibly go with; not much development, but he's incredibly expressive and has his own distinct personality. Mario, regular Link, Luigi, etc, would instantly be off the list for me. Possibly Samus, as there's a fairly detailed backstory behind her that does explain her characer and lend her silent personality a step ahead of the usual quiet protagonist stereotype.