You can't frame the question of smash's roster through a lens of Metroid's importance to Nintendo's history. There are so many characters from so many fandoms, many of which with legitimate claim to the roster, and Sakurai is not a biased man. In fact, he is very modest.
You really have to step into his shoes as much as possible. Lets frame together what we know.
From brawl we know that he is actively looking for ways other than playability to represent more of Nintendo's history, because he really cares about every fan, and doesn't want them to feel left out. Since there is no Emissary, there are not going to be boss characters this time around, which limits some of his representative resources.
However, stage hazards are still a large part of the game. More people play smash causally than competitively, by a longshot. Including a character as a stage hazard, from that standpoint, is much more than any assist trophy gets. Sure, it's shy of playability, but he's trying not to kill his dev team, let alone himself, with terrible chronic pain in both of his arms now.
I feel like from his stand point, while it may be disappointing to not make as many playable characters as he wishes, this is a ridiculously large game, there is so much to balance, and some sacrifices have more silver lining than others.
So please, from the perspective of a game developer, do not question Sakurai's competency, regardless of roster inclusions. There doesn't always have to be someone to blame. I doubt he's purposefully made any inherently wrong decisions about the game's content. On top of all of that pressure, Sakurai still makes sure to squeeze in an element of unpredictability, wii fit, because that is his style. It's part of what makes smash smash.
/rant