I see few people are sticking up for red side here, so let me take a crack at it. *cracks knuckles*
Red side was always home to me for some of the reasons highlighted above as reasons to NOT play there. I found blue side to be too clean-looking, too artificial , red seemed much more solid a place - not gritty, just more lived in.
I enjoyed the way your character was channeled across the various islands as they leveled up, giving you a real sense of a path to, well, infamy I suppose. The islands also allowed the devs to put in a more varied map, not just an endless cityscape; over here's some city that looks less like a row of featureless glass boxes, then a mountain, some industrial areas, an old castle, a wharf, etc. I know blue side had all that too, but it had less of it to my eyes, red side felt more varied, more different areas packed into a smaller location.
Mercy island was a sort of obvious "starting with nothing in the gutter" place for you to rise up from, so the dismal look was fitting and ha ha, gave you a reason to want to get out quickly.
I preferred the character classes better for some reason, perhaps because they were a bit more complex to pull of in action.
Something red side lacked? No Hollows. That place always felt like some kind of pointless punishment for such low level characters and my first encounter with it almost put me off the game as I was learning how to navigate the world.
I'll concede that it never felt quite like really being a "true villain" though, but for the same reasons (contacts directing you instead of, I don't know, heading out on your own somehow) blue side never felt too much like being a real hero either. I wasn't so much invested in the story on either side though, my characters were who they were rather than fitting neatly into the hero/villain dichotomy.
Near the end I did end up playing blue sidesome, but only because the game population was shrinking so far that even on the most populated servers I couldn't find anyone to team with. If I'd have been able to, I probably wouldn't have left red much at all.