Yeah, I've wanted Reptile to remain the green ninja forever. I think once they literally made a walking lizard I didn't love the character anymore. He went from being a super cool and VERY mysterious badass threat to a gimmicky pawn or henchman with a tired and drawn-out backstory. Reptile is one of the characters that the more background of him is created, the worse it gets. Mystery was what was so intriguing. I kind of feel the same way with Scorpion, but at least I do care about his story unlike Reptile. Sub Zero, the ice powers, was always a fitting and perfect background.
Noob is a total badass, I just hate the name. I like his storyline (how he wants to rule the Netherealm and his tension with his younger brother) but I hate how MK9 story mode treated him. He got school too easily and too often. Smoke is still pretty bad ass because they are still trying to keep him very mysterious. He has an ending since he has to have one but I don't feel like I know much about him, like a proper ninja. Maybe I'm expecting too much from the story of these games (okay I know I am) but I love the mythology created for these game, and I like what MK Legacy did with them. Way better than the movies.