Alright, don't flame me for this, but I think I know why this could be true.
For one thing, adding Mewtwo to the lineup would NOT give Pokemon more reps than Mario, or in Sakurai's eyes at least. Icon-wise, it would, but look at the clues, people. Sakurai never expected to make a sequel to his low-budget N64 game called "Super Smash Bros." Heck, it wasn't even supposed to leave Japan. That's why he gave Mario and Yoshi different icons, even though they were technically from the same game. In Melee, there would be no reason to drop Yoshi's egg and give him a mushroom, so they kept the egg. In Brawl, Wario was added and given the Wario "W", even though he is primarily still a Mario character. The way I see it, in Brawl, Sakurai thinks he put in six Mario reps: Mario, Luigi, Peach, Bowser, Yoshi, and Wario (Donkey and Diddy don't apply, as they actually have their own series of games, while Yoshi hasn't had a game to himself since Yoshi's Story; Wario might be a bit of a stretch, though). If Mewtwo was added to the lineup, it wouldn't make a difference because Pokemon would have 5 reps, Zelda would have 5 (with Sheik, 4 without), and Mario would have 6. Roy would just be icing on the cake for FE fans. Besides, Roy was more popular to the casual player, the players that don't post on forums like these. For all we know, the people who like playing as Roy might be bigger than those playing Marth or Samus. Taking out characters just disappoints people, anyway.
Just a hypothesis.
EB08