A few things.
1. As I've said before, we're not going to sit here and talk about of Myths and Monsters like it matters unless we're going to say Orcos is a major contender for Smash Bros., and a US-exclusive game in a series of international releases is going to be the part of the series a japanese developer cares about the most.
2. I wouldn't even say Palutena was THAT much more important than Medusa in Uprising. They were both essentially equal in the first for all intents and purposes with MAYBE Medusa having the edge, but that's really picking at NES limitations. Uprising, we're comparing two characters.
- The "helper" who for a large part of the game basically just kind of talks to you. She's a major character in the story, but at the same time for a part of it she gets swapped out for Viridi who does the exact same thing just as well. She also gets canned a bit for the Chaos Kin arc as well as the Dyntos boss gauntlet.
- The first arc antagonist who was the main villain for the first 9 chapters; more than any other antagonist in the game can really say. Also unlike other final bosses, she was in almost all of the promotional everything and even got the animation based around her. And even though she got "used up" as an antagonist for the game, she still came back to participate in the final battle.
In Brawl, we can't really use that here. Since it happened before Uprising, of course Palutena is going to come up more than Pit. She's his final smash. Medusa isn't about to be Pit's final smash. I have no idea why she would have like 10 trophies or anything. And if anything I feel like Palutena being Pit's final smash is more of a point in Medusa's favor than anything. If I had two choices: A more unique character for less work or a less unique but more popular character for more work in a game where I was putting emphasis on uniqueness, I know which one I would be picking.