I think Metroid is only considered to be one of Nintendo's main franchises because it was one of the first. In classical terms, there was this trinity: Mario, Zelda, Metroid. Of course, Metroid never gained the world-wide recognition the other two did.
Anyway. Over the years, the Metroid franchise is at 17.49m total according to this site, while Pikmin is only at 3.78m. At least Pikmin won't overtake Metroid's lifetime sales this gen. I agree it's likely that Pikmin 3 will sell better than whatever Metroid game comes this generation.







