Medusa may have the advantage of seniority, but she's not exactly a character of high priority in the series. She was the main antagonist in only the first game as a pathetically easy boss, completely absent in the second game, and a glorified scapegoat for
in Kid Icarus: Uprising. The latter is also important to take note of since Kid Icarus: Uprising was directed by our good friend Sakurai, but wasn't involved with developing the first game in any shape or form. The only reason why she
appears to have such a big role is due to advertising for the game, but to only contain the surprise plot twist after you beat her and supposedly beat the game.
I do understand why she could theoretically be a playable character since she's the dark counterpart to Palutena, tried to take over Skyworld, imprisoned Pit and the centurions, and all that mushy crap, but that doesn't mean she would be a high priority for Sakurai as a character.