Alot of what I'm seeing is people complaining about a lack of Metroid characters. The Metroid games are great and deserve Smash Bros representation, but you can't just throw in a far-fetched character like Dark Samus just to increase the number of Metroid characters. In fact, one of the key aspects of the Metroid series is the lack of characters. The games are primarily about Samus exploring alone, with most of the enemies being the planet's wildlife.
Zelda can have many characters because every game since Zelda II has been about encountering and speaking to a variety of characters. Mario can get away with so many characters because it's Nintendo's flagship franchise and most of these characters have earned full spin-off games and franchises. Every Metroid game, however, has been about Samus by herself (and I feel that the Prime series is straying too far from that, but that's a debate for another time). Therefore, having few Metroid characters isn't a betrayal to the brilliant Metroid series, but is actually a testiment to what it stands for.
The only other characters that are central enough to Metroid (meaning appearances in multiple games, importance to the overall plot of the series) would be Mother Brain, Kraid and Ridley. Ridley is the only one of these, though, that would work in a Smash Bros game, but I'm sure you already know this. Dark Samus does not fall into this category as she only appears in the Prime games, which plot-wise acts as nothing more than an overglorified sidestory to the regular Metroid games that tries to paint itself as more important than real games of the series like Super Metroid or Metroid Fusion. Really, Dark Samus would not act as a good representative of the Metroid franchise in Brawl and to put her in just to have more characters from Metroid games would go against the ideas of the Metroid and Smash Bros games.
Wow, that was alot longer than I expected it to be.