I don't know if you've visited r/fitness or r/gainit, but metabolism really only accounts for a variance in about 200 calories. The big thing holding skinny people back is that they pretty much aren't eating enough of the good stuff - sure a skinny person might eat 3 cheeseburgers in a sitting but it doesn't help that their only exercise is cardio, or that it's the only substantial thing they actually eat all day. Many self professed skinnyfat people who claim they eat like a horse are shocked to find that they aren't consuming nearly as much calories as they think they are when it's all being tracked.

Did you actually religiously track your calories in/out?