Your argument doesn't hold up to experience. The JJ3D game had plenty of good reviews here, and a widely different reception than JJGBA. Some people might not play it because it'd probably be a 3D platforming game and they are not fond of such but these people would probably not play any 3D platformer.

You mention several franchises with a different experience but these are much more popular games with a much larger base. I think the Mario universe is so much more set in stone than the JJ2 universe, and much more considered canonical (sp?) that it's easier to have a major reaction.