Let me explain. In just about every story, there's the "Big Bad". There's always some evil presence that acts as the antagonistic foil to the heroes: the dark lord in the midnight castle, the scheming supervillain planning world domination, and so on and so forth. In this case, we have Medusa, the Goddess of Darkness. She turns people to stone, poisons rivers, sends hordes of infernal monsters to terrorise the land and generally causes chaos and madness. She's pretty self-evidently the bad guy.
Then we have Palutena, the Goddess of Light. Palutena is the polar opposite of Medusa in every conceivable way: Medusa is a grotesque demon, Palutena is a beautiful woman; Medusa is a calm, sinister evildoer, Palutena is a lively, vivacious force of good; Medusa is dark in her colour scheme, Palutena favous bright tones; Medusa commands death and ruin, Palutena orders life and honour. They're both exceedingly different.
That being said, look at them a little closer and you'll notice that they're actually a lot more similar than their initial appearances may suggest. Both are goddesses that oversee the world before them, each one maintaining dominion over a certain key element of existence: light and dark, good and evil, life and death, white and black. The two are not mutually exclusive, as they are, rather, two sides of the same coin, so to speak; mirror images of one-another. They even wield similar staves, and both are wielded in the other hand!
What's really cool, though, is that neither of them are presented as being obliquely "good" or "evil". Both are equally grey in certain areas.
Medusa is a cruel, merciless bringer of terror and destructive power, but she is only reacting in a human way - she has been mocked and scorned too often, to the extent that she has become a force for evil. All she desires is cold, calculated vengeance on those that made her the way she is. She appears in the climax to knock off Hades's final blow, so tired is she of being his mindless servant that she displays that most human of traits: free will. Regardless of whether she willingly chose the paths of evil and darkness to begin with, she has elected to become the symbol of all that she has been depicted as. She is the embodiment of evil not because she wants to be, but because that's just how the world sees her.
Palutena, conversely, is a hero with a lot of grey smeared into her pure whiteness. She is the ruler of Skyworld and the protector of mortal beings; the very embodiment of justice and honesty. That being said, let's consider some the things she does throughout the course of the story: she turns Medusa into a wicked abomination to reflect the evil in her heart, thus creating the very antagonist that becomes her arch-nemesis in years to come; she purposely sends Pit into dangerous situations, confident in his ability to succeed against all odds, but seldom intervening herself; she willingly and happily teases and tricks Pit whenever the situation calls for it and never apologises for her bizzare, juvenile behaviour; she rejects Magnus's cricitisms of her handling the Underworld invasion, citing him as "a jerk" for not conforming to her bleak, cynical standards of humanity; she causes a lot of mischief and has a tendency to disregard the true danger of what she is doing to Pit and others as well; she is arrogant, petty, spiteful and lethargic - hardly qualities we'd consider to be "good"!
And that's why I love her so much. She isn't the all-encompassing, incorruptable effigy of truth and light that so many "Big Good" characters are: she's fallible, she's corruptible, she's weird, she's messed up in all sorts of strange, humanistic ways. She makes mistakes, she breaks down, she has flaws, she isn't as strong as she's made out to be. She's the embodiment of light and the paragon of virtue to mortal beings; but to other deities, she's just another goddess with a lot of responsibilities and her own personal agendas to accrue and maintain. Pit regards her as the saviour of creation and the greatest person in existence, not out of coercion or irrational judgement, but because he genuinely loves and cares for her. Palutena's job is a hell of a task and it's clear that, for all of her divine powers and cosmic levels of egotism, she suffers and cries just like everybody else does. Pit sees her for what she truly is and he doesn't mind: he sees past the good and into the darkness of the abyss and sees it staring back at him, the true, essentially human aspects of her; and then beyond even that to see the real good within her, not just the projected, reflected good.
Palutena, in my eyes, represents true good. She is the sort of good that doesn't care if it's weak and ill-equipped, if it's foolish and naive - it's good for the sake of being good and because it's the right thing to do. To err is human, to forgive is divine: and no godly paragon of good and saviour of justice is truly divine without being just a little human.