Yeah, this thread's just going to agitate people.
Anyway, these sorts of questions are so subjective and arbitrary. Especially this one -- we're evaluating characters, not games. So a lot of the response will be driven by a different question entirely -- "How important is story in your games?" Or maybe, "What characters symbolize games you like?"
So. To respond. As to the characters that I've seen mentioned, I agree that Mario's overplayed. I like Master Chief, though I think he's far from the most interesting character in the Halo games. Of course, I love the Halo games, and I've been a Bungie fan since looong before Halo, all of which is bound to affect the way I respond to the characters.
Can't comment much on the Final Fantasy characters people have mentioned, as I have a strong aversion to all things Final Fantasy (which generally makes me something of a pariah among gamers
).
I'll bring up the potentially dangerous topic of Link -- my Zelda history is spotty at best (I've played the original LoZ on the NES and Wind Waker on the GC) but I've always been a bit baffled by the extent to which people adore and embrace that character. I mean, he doesn't even talk, right?
Same goes for Samus Aran -- people just fawn over that character. I'm not sure why. I think the bottom line is you'll like characters from games you like, and dislike characters from games you dislike. It really doesn't have anything to do with the characters themselves. I mean, both Master Chief and Samus Aran are essentially suits of armor. Whether you like one or the other better likely depends on whether you like Halo or Metroid better.