MoR Harry did seem like a Marty Stu in the early chapters, but the further I read, the less I thought so. For one thing, his intelligence is balanced out by egotism, insensitivity, and inability to think in the longterm. For another, most of his really impressive feats of intellect and willpower are actually owed to Voldemort's horcrux (his "dark side"), which means Harry doesn't get full credit for them. I think MoR Harry is far from perfect.

Wait... you don't attribute dark side Harry to Harry? Damn. They're the main parts I empathize with!