Oh, and gut character rankings:
Phi > Sigma > K > Luna > Tenmyouji > Alice > Dio > Quark > Clover
Phi and Sigma in particular are at their best around each other. Their banter was some of my favorite stuff in the game, and in-story it was really fun seeing them trying to make sense of what was going on. But they're both awesome on their own.
K could be a jerk at times, but at the end of the day I think he wanted to do well. His ending was one of my favorites, and his backstory is really a tearjerker, especially when you know who his father/the old woman/his robot 'mother' are.
Luna sort of felt like "June" done better. Above all she was a good and kind person, but you still had room for suspicion. Her backstory was pretty tragic as well, and the entire ending portion of her path when Sigma and Phi are trying to figure out if she's a killer is really great.
Tenmyouji was an interesting character, and it was fun to see bits of old Junpei poking through (the discussion of his videos and the like), and of course the scenes in the Q room and the B. Garden at the end are really something. A really big chunk of his time was spent on Quark though (who I didn't much like).
Alice was a pretty decent character, but she sort of suffers the same issue as Quark in that so much of the time her story get sort of cracked down on by Radical 6. I was also a little disappointed that her backstory had nothing to do with All-ice and that she didn't have too much to her backstory besides what I'd known from Japanese promotions. But the scene in the B. Garden of her breaking down after trying to betray Sigma a second time was really well done.
Dio is... well, he's an asshole through and through. As far as villains go, I much preferred Ace, who had the great, nice-guy front over a truly merciless core. Still, his backstory was moderately interesting, and his ending was much better than I'd expected (I figured he'd just off Sigma and Phi once they got through the door, but nope.)
Quark kind of suffers as a character because he spends so much of the game unconscious. Even when he is awake and not insane, he doesn't really do much except bicker with Dio if they pick betray and make a bunch of references to Tenmyouji. I mean, if I'm not miseremembering, the only puzzle room you solve with him is the Director's Office. Also, his ending is really abrupt, though Sigma making Dio drag him to the 9 door so he could cut off his hand was an awesome scene.
I feel kind of bad for putting Clover at the end, but I thought she was a lot weaker in VLR than 999. In 999 Clover was genuinely sympathetic after Snake's death, but after Alice's she just goes around raging at everyone. I mean, she did in 999 as well, but in VLR it just sort of got grating. She also had the weakest VA of the group.
