It does really well when listened to as just a music piece. J-E-N-O-V-A is one of those video game themes that feels frantic when it's not being used as a fighting theme. Listening to it without anything going on doesn't work as well.
You're Not Alone; I have a bit more liking to this song as a whole than to JENOVA, but part of me does feel that JENOVA is the better choice.
If I could have it my way, I'd have JENOVA be the epic boss theme to make it to the semi-finals over One Winged Angel, but that's not gonna happen, so I also think You're Not Alone is a bit overrated. Difficult decision but... I've made it and hope I don't regret it.