1. All of these are just assumptions, they make sense but in the end, they still aren't facts. We don't actually know why Dixie, Roy and Mewtwo were cut, end of story
2. Pokemon is a flagship series of Nintendo, lol, I don't think you realize just how big Pokemon is in reality (it's the 2nd biggest VG series out there in terms of sales, only second to Mr. Video Game (Mario) himself, and Pikachu I'd say is pretty iconic since it was part of one of those Thanksgiving Day Parades alongside other well-known fictional characters)
3. Smash isn't that corporate, if Sakurai wants 6 Pokemon reps and 5 Mario reps, then he'll do it, the number of reps shouldn't really be judged by a series' popularity, anyway, except in extreme cases, maybe
1. They would be assumptions, had there not be hard evidence on Mewtwo and Roy being scrapped late in progression.
They are the only scrapped characters of the "Forbidden 7" to feature their own files for their own victory jingles, and Mewtwo supposedly has extra files that not even Roy has. Sakurai has also stated that there were a few characters he was not able to include due to time restraints.
2. I don't think YOU understand. I did not say Pokemon was unimportant. How ironic that you denounce my words as assumptions, yet you make some of your own right here.
Mario is THE flagship series of Nintendo. Mario is THE main representative of Nintendo. While yes, Pokemon is the 2nd biggest series Nintendo has to offer, to honestly believe that it would ever sarpass the 1st is foolish, no offense. And remember that Pokemon is not fully owned by Nintendo, but a 2nd Party company/companies (GameFreak and Creatures Inc.). 1st Party IP > 2nd Party IP. 1st Major series to Nintendo > 2nd Major series to Nintendo. It's just common logic. Pokemon will at most have the same number of characters as Mario. End of story.
Now, there are fools who believe that Squirtle, Ivysaur, and Charizard count seperately, but they don't. They all count as part of the Trainer, who is the REAL character that is being represented.
3. "the number of reps shouldn't really be judged by a series' popularity, anyway, except in extreme cases, maybe".
Quite unsure of yourself, it seems.
Anyways, this doesn't even matter. Mario vs. Pokemon doesn't come down to popularity, because honestly, I believe Pokemon is much more popular, given all the exposure it gets with the anime, the card games, and merchandise outside of the games themselves.
It comes down to which of the two is more important to Nintendo. And the answer is Mario. This cannot be denied.