As someone who disliked Marcus: no way was he a Canon Stu. That's what the guys with the initials J and S were there for! :)

I think you're on to something with "young male character who represents what nerdy fanboys dislike in themselves instead of what they fantasise". Wesley (and Adric) were never "cool". Jake and Nog were spared that ire because they never were as visible in the show; well, Nog was in the late seasons, but but of course by the time he was a member of the bridge crew of the Defiant, we'd seen him work to become the first Ferengi in Starfleet for several seasons. Whereas Wesley made it to the bridge within the first season.