He's the only protagonist who has been recognized as a champion. Proof? You actually battle him in the Champions League of the PWT in B2/W2.
You don't battle any other protagonist.
By making him the Ultimate Challenge, it just proves how great he is.
Not to mention the fact that he doesn't speak, it's condescending behaviour. Implying that he is too good for you.
Red was popular before Pokemon Origins, though - in fact, Origins was made because of Red's popularity amongst older fans.Also,he is the strongest one and has his own series (Pokemon Origins)