You could use that argument about many of Melee's characters. Ness shouldn't be in, he has the same basic attacks as Mario and looks similar too (blue pants, red hat...)FTR: It doesn't matter if Dark Samus is her own character, she still looks exactly like Samus and uses the same basic attacks.
Dark Samus is pleanty diferent, from flying, to her phazon shotgun to her phazon blast in the final fight in MP2...she's very diferent.
Her armour is part biological. The X Parasites in Metroid Fusion grew and replicated multiple SA-X's (Samus parasite clones) with complete armour and weapons.One more thing, Gypsy: Dark Samus isn't PURELY Metroid Prime possessing Samus's Phazon Suit; Her scan data shows a body underneath the armor, and it's clearly female. Except she has no right hand; It's just a hole for the arm cannon. Metroid Prime took up the appearance of a girl, not just her armor.
Anyway, each character already has a topic, why do we need yet another topic on them?