Three years ago, my ballot vote went to Dark Samus. I would love for her to be a totally different character, but I'll
enthusiastically settle for an Echo Fighter. Just change some of her animations and effects and she'll be my new main, hands down.
Anyone who says Dark Samus doesn't fit as an echo fighter is being delusional. Now whether she is popular enough to get into Smash is a different matter.
Supposedly Dark Samus/Metroid Prime isn't going to be in Metroid Prime 4, so that would be a funny way to promote the game. Or maybe (hopefully) she will be in Metroid Prime 4, because let's be honest, a Metroid Prime game without the Metroid Prime herself is dumb.
"Prime" is more a designation of a specific brand/style of Metroid than it is associated with a character now. Metroid Prime: Hunters and Metroid Prime: Federation Force have nothing to do with the Metroid Prime creature, but they denote that they exist within the story bubble of the Prime setting and share much of its style or gameplay, as opposed to all the other Metroid games, which belong to a different style and gameplay. I highly doubt Dark Samus will be in Prime 4, though, since Phazon is apparently eradicated at the end of Prime 3.
It wouldn't be the first time a series created a title for itself that had such a specific association, and then ditched that association as they needed to expand. Halo is a good one, as the number of Halo games that actually have a Halo in them is now smaller than those that do.
That said, Dark Samus would still be a good representative of the Prime series, as she/it was the final boss of all three games in one way or another. If they wanted to advertise 4, they'd use Sylux, since he's been teased for a major role twice at the end of 3 and Federation Force, but he was only a minor character in Hunters. Though I sincerely doubt the new characters are going to be used to promote new or recent things, but rather the characters are going to older but hotly requested ones, like Ridley, Daisy, and Cloud. Not only that, but Prime 4 is still a ways away, and we don't know anything about it for sure, so no character inclusion is going to do much good right now.