Counterpoint: Series Mascot =/= Protagonist
If I showed this picture to any random person, would they know what game it is?
Now imagine this one:
Aww, remember when he used to be tubby?
Remember - there is
one set of games (okay two if you include the Coliseum ones) that you can't get a Pika in, and that's the B/W set. How many old people do we like to joke about who think that
all Pokémon are called "Pikachu?" It's completely reasonable that they would have picked Pika over Red.
The one area where this argument starts to break down is the DQ Hero, since the Slimes are more well-known than the protags. But I'll also say that in DQ, your character is still the one doing the fighting, not the slime (and someone correct me if I'm wrong, I don't know DQ at all). In Pokémon, your character runs around the overworld, but the mons do the fighting.
Maybe Jiggles over any other mons is the weirder choice, or Pichu, but both of those were clones of existing characters. Also Mewtwo was a weird choice before Red or Charizard, but again - Red doesn't really do anything in the series other than walk around, it's the mons who do stuff. And as much as people don't like it, the way Red is in game now with the switching mechanic is about the most faithful they could get for the series.