Who do you think is more evil.
I think that Medusa had a greater contrast than many of the bosses in the game. She was not only evil but also a kind of tragic character having a strong hate for Palutena and she ended being Hades puppet. Also she didn't made silly jokes in the conversations.
In regards to Hades, well, I thought he was only acting his part as an evil villain. Most of the dialogue between him and the heroes were hilarious teases, he really like playing with them. I also felt he felt Pit was more of a buddy than an enemy. Hilariously unfitting dialogue right at the start of an epic battle.