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You got a point there. And I'm a Paper Mario fan, so I like seeing what they do with telling a Mario story. That being said, all of the Paper Mario games (and the Mario & Luigi games) keep one thing consistent: Mario is a flat character. He doesn't grow or evolve, though everyone else is fair game (including Luigi). That might be the sticking point here: Flynn is treating Mario as a normal protagonist.
From what I can remember though, Miyamoto was not happy with how the Paper Mario games were going, and he was quite upset when the staff of Super Mario Galaxy snuck in Rosalina's storybook behind his back, such that he ensured it wouldn't happen again for Super Mario Galaxy 2.
I actually see a great deal of Mario merchandise, but because Mario is such a blank, flat character he may have undergone the same issues as Mickey Mouse in that there's nothing that really stands out about him to people other than the brand name recognition and the quality associated with him. (That being said, Walt considered Mickey as too bland a character to use much.)