They really aren't options. All of them are one-shot characters with little impact in the Metroid series. I stand by my opinion: Dark Samus and Ridley are the only characters in the series that would make sense as the third (second, actually) Metroid rep. Rundas or Gandrayda would be stretching a lot, but since I like these characters, I wouldn't mind them in Smash... after Ridley.
And really? In a game in which four Samus can fight each other at the same time, the fact Samus and Zero Suit Samus have separated slots is what bug you?
Zelda from Twilight Princess transforming in Sheik didn't make any sense in Brawl, the Zelda who can transform in Shiek is the one from Ocarina of Time. Now that Zelda and Sheik are separated characters, it makes way more sense. To me Sheik in SSB4 = OoT!Zelda transformed. We have two Zeldas in the game now.