Regarding the Mary-Sue hero....
Instead of making him only a jab at Angsty heroes, what about actually fleshing him out so he doesn't end up as whiny, and potentially give him his very own badass moments?
But first, his weapon. We said he had a sword, right? How about a Runic Sword of sorts, one that, at first sight, looks like slab of rock taken straight out of an ancient ruin filled with words in an ancient language. He uses this sword, at first, just to bash things with it, but later realizes that it can be used to channel one's magical energies to reshape the rune and the energy within it, giving him access to several weapons. It would also work as a catalyst of sorts.
As for his story, let's not have him realize he isn't the hero at the end of the game. Instead, he is told about it 1/5 into the game by the Wise Bird Guy himself. Instead of having a breakdown, like a pussy, he gets a breakdown like a man and starts beating your shit up because, regardless of his lame, bitching and angst, he IS better than you at most things, personality notwithstanding.
He then takes off and he stops being a permanent party member, appearing only at convenient spots to advance the plot and help you with the hardest fights, getting into fights with you in the middle of boss fights and generally changing from being helpful to annoying. He doesn't join you officially until near the end of the game, when he grudgingly accepts that you are better than him (your character eventually becomes the strongest, bar none), but not before you beat his shit up and slap him to wake up. However, he still hates you and his brotitude becomes 0, and you never really become friends. After the end of the game, he just goes away without saying a word.
As for his stats, he would have high stats (being a Mary Sue) probably the second or third highest. His main stats would be Magic and Strength, with the rest being higher than average.