Nah, Mother Brain is only in Metroid, Super Metroid, and Zero Mission. and Ridley was prominently featured in Metroid Prime, Metroid Prime 3, and Fusion, which all sold over a million copies, in addition to the three aforementioned games. And since I doubt many players who played Super actually got to Mother Brain, they know Ridley from the well-known introduction sequence. Same with Prime 1 and 3.
And the Melee intro, too.
edit: oh, forgot about Mother Brain in the Other M intro. Eh, I don't think anything from that game will be labeled "iconic" (at least not in a positive way), but the Mother Brain sequence it took from Super Metroid certainly is. Still think that Ridley is a much more prominent character from the series.