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.

You're totally right about the house system, though. That's why I really love the subplot about Quirrel's armies; it breaks up the house system and lets all the students interact more. I'm so glad we got to know the Slytherin girls...