This song is actually really tear-jearking.
No, I'm serious. Listen to this version and the Crush 40 version with the idea that the character singing their version of this song and all of a sudden there is a plethora of meaning behind practically every word of this song.
"Dark Queen" Merlina: Her version of the song is a faux condescending speech towards Sonic as he stands before her. She tries to convince herself, and by extension, Sonic that what she doing is ultimately good in the end, even if her plan involves defying the very thing that life and nature stands for. She understands that things will inevitably end and thoroughly believes that she can stand in the face of it and come out on top. Merlina doesn't want to accept the destiny of all things (which is that everything will come to an end, one day or another.) and she pretends to accept a wicked persona believing that if she is indeed evil, she will succeed. Sonic, however, still wishes to argue against her. Sonic, a person that she has immense respect for, stands in front of her as an embodiment of her conscious. He knows she's wrong, Merlina knows she's wrong, but she believes that she can go through with it anyway, which is how she ultimately clashes blades with Sonic. She dares the hero, Sonic, to try and stop her because if he can't, then 'supposedly' nothing else will be able too. There's also an obvious sense of regret in her "voice" during all of this. To her, Sonic is the hero that she cannot be. Her inability to be strong in the face of death (pretty much) is why she calls herself evil; It's her wicked deeds that the world will condemns and she wishes she was as strong as her hero, the one person she had hoped to understand. She essentially becomes wrong for all of the right reasons.
"Knight of the Wind" Sonic: His version of the song is a bit of the opposite of Merlina's. As he stands before, he realizes that her insecurities are born of common, everyday, fear. Something that he has come to terms with and accepted. In this scenario, Sonic still believes himself to be the villain. Why? Because he completely, COMPLETELY understands her motivation here. The pain of loss and the knowledge of the demise of everything you love is something that everyone experiences. And she seeks to END that suffering. Sonic is actively robbing the world of it's chance to be eternal. The villages he's saved, the people he's met in this world, this is him guaranteeing their expiration date. To him, Merlina is more of a hero because she is doing everything she can to bring about something that many would consider an ultimate good. If this is so, then he obviously wouldn't want to stop her, right? Wrong. He knows that her goal is insane, that her ideas are corrupted by fear. She's the one that needs to learn, and Sonic can only teach her by showing her why. Notice the way the song's being sung in this version; Crush 40's normally aggressively bad-ass tone is a lot more subdued and incredibly mournful. He doesn't want to do this because he knows the message is sad. "All things die. It sucks, but you can't stop it." Who in their right fucking mind would want to deliver such a depressing, almost disheartening message to anyone? That's why Sonic sees himself as the bad guy; He's going to bring about a suffering that, while is ultimately good, is also incredibly tragic.
tl;dr These songs compliment themselves really well if you listen to them in the context of the characters that would be in the scene at the time they play. Uncannily so, even. I almost wonder if that was intentional...