I was going to make a joke about Shin obviously not being a Mary Sue, but I just can't get past the general conceit of the game. I mean, as Vendrin says, we're all immortals who control spaceships with our minds. The poorest of us are fabulously wealthy. Hundreds (if not thousands) of "mundane" people die on our whims. No Mary Sue there at all.
Surprisingly (to me, at least), I don't see a lot of Mary Sue in Eve. It was my first "real" MMO, and when I first started I was amused by what I saw as the rampant Mary Sue-isms. All the living gods striding among the human worms, and all that. Then I took a break and played a few other MMOs, where I came face to face with reality. I think it ultimately comes down to pvp. Eve revolves around pvp, to the extent that there is almost no way to really avoid dedicated attempts to pvp you. If someone wants to shoot Shin, they will find a way to shoot her. This automatically cuts off a huge swath of potential Mary Sue-ism. We've all played (or heard of) games filled with people who love to RP unbelievably deadly killers. It's one of the staple Mary Sues of MMOs. It's easy, in most games, to claim this because there are few options to translate that into actual game actions. In Eve, it's different. If I play Shin as an unbelievably deadly killer, I'd better be able to back that up in game. At the same time, if Shin is an unbelievably deadly killer, then that fact speaks for itself without any claims being needed.
It's like Istvaan. In any other game, if you ran into a character that claimed to have organized the downfall of nations, you'd snort to yourself and go "sure". In any other game Istvaan would be a Mary Sue of titanic proportions. In Eve he is not, though, because in Eve he actually has organized the downfall of nations.