Only done Aselia, Esperia, Lesteena routes so far, but my choices for now are:
Nelie - Early on, I wanted to choose her for all 3; I like her better than Helion and she's awesome in gameplay (well she was awesome at the very start, then sucked until around the 2nd half of Hard when I needed her high level interrupts and she got HSIII). Makes me very unhappy that she got so few scenes compared to the rest of the subspirits, I really hope for Spitan to be translated so I can get more Nelie.
Esperia - If not for the fact that I'm skipping text now and thus don't see Yuuto's interaction with her anymore, I think I'd feel sad about abandoning Esperia on every other route. I felt that way on my first playthrough (as did Yuuto, was amusing though when Aselia got jealous on the way to Kihanore) and I definitely would now that I've played her own route. The combination of her being such a perfect wife and her traumatic past makes her impossible to resist (now if only she had some "resist", dohohohoho)
Kouin - He's just too awesome, though admittedly sometimes he was almost too perfect (although I hate to throw the term Gary Stu/Mary Sue around), like how completely rational he was dealing with their appearance in Phantasmagoria and subsequent capture, being able to wield his sword with no hint of problems like everyone else had (maybe Karma was just a nicer sword than the others, I dunno). Of course that's also why he's stuck being a side character while the flawed Yuuto is the main character, as Kouin amusingly bemoans at one point.
Lesteena - Nothing special until playing her route, after which I feel bad about ignoring her almost as much as I do with Esperia. Her route was so depressing and at the same time annoying though; as people already warned me, it has the least content (though it makes sense why it's that way), and...
Io - I was really mad when Lesteena route had no extra info about Io, just that fanservice scene (damn, she is the sexiest spirit, though of course it helps that that scene is newer art). I thought for sure the 3rd playthrough or Lesteena route would have more about Youtia/Quedgin/Io, but I guess Quedgin's flashback and the enemy Io's status/skill descriptions are all you get