Truth be told, it doesn't, except insofar as you would generally prefer to be on the more populated faction. The fact is that outside of some flavor differences, there's not a whole lot of variance between the red side and the blue side any longer.
This didn't used to be the case, at least not to this degree. But part of that was because we had two completely different sets of endgame Task Forces, and that was the only real ending mark available. Farm up some merit rewards and money and maybe raid Hamidon if you really felt the need. You had to do a bit more work to get your epic pool unlocked on red side, but everything else was kept functionally similar. Break into a bank, don't let people break into a bank -- how different are they?
But even so, there was a sense of separation. Part of it was that there were seven classes you couldn't play on the other side with unique sets of abilities, and part of it was the fact that the flavor was always different for you. There weren't a lot of unique elements at the endgame, but they were still there.
Now, of course, the endgame system is the Incarnate System, and that is all universal to both sides. Moreover, there's a distinct in-game benefit to maintaining an alignment repeatedly rather than swapping back and forth. If you like hunting badges, you'll want to go all the way around at least once, but otherwise you're best served by picking a side and sticking with it all the way through. Grab some tips and some alignment merits on the way and craft some high-end sets when you hit the level cap. All of the missions you really want to run are available to both sides anyway.
It's the Marvel Comics problem. When you blur the lines enough and give everyone no real reason to be a hero or a villain, it's either going to change at the drop of a hat or just cease to have any relevance. Whatever distinction the factions once had is lost amidst a sea of shifting allegiances.
The problem, of course, isn't unique to the alignment system. The fact is that the villain side has never felt super-villainous. I don't think anyone really wants to be taking part in missions in which you chop up Sister Psyche and stuff her in Manticore's fridge, but the structure of an MMO doesn't lend itself terribly well to supervillainy. There are only so many ways to write in a failure to take over the world, after all. You aren't playing Doctor Doom so much as Undergraduate Doom, whose big plan is to break into Reed Richards' house and wreck up the place.
But the big thing is that the game built two conflicting design goals into the alignment system. I can understand why Paragon chose this route, after all -- you want to sell this feature to people who might very well ask why they ought to care. So you give everyone some incentive for doing alignment missions, including special rewards for sticking with a specific alignment if you don't want to change, and... um... well, no real incentive except the uniqueness of changing if you decide to change.
In other words, the central feature of the system seems just a touch pointless, and the rewards for sticking to a single alignment are pretty substantial, which means that you get the best rewards for not using the system, or at least not using it for the actual purpose of switching alignments.
This isn't a totally bad thing. For one thing, it means that my potential doomsaying about certain archetypes overtaking others hasn't come to pass; the archetypes that were always poorly represented remain so, but if anything has really changed it's been that Masterminds are now more evenly spread across both factions. It also means that we haven't seen a dropoff in content for one side or the other. Instead, the developers are actively pushing to make sure that for every new thing on one side, the other side gets an equivalent. Yes, the precedent had been set before, but it's something that could easily have been abandoned with the premise of "if you want to see this you have to be a villain" or something similar.
Still, overall, I'm looking back at the system and noticing that even I don't really use it in depth. I touch upon it, I swap to the alignments that I think are appropriate for the character, but I don't find myself really going back and forth. It's a nice feature, but time has not proven kind to its overall utility.
As always, the comments below or the usual mail address can be used for feedback. (It's firstname.lastname@example.org. You know that.) Next week, I'm going to take a look at another enemy group that spans the length of the game... even if they seems like they ought to drop off fairly early on.
By day a mild-mannered reporter, Eliot Lefebvre unveils his secret identity in Paragon City and the Rogue Isles every Wednesday. Filled with all the news that's fit to analyze and all the muck that's fit to rake, this look at City of Heroes analyzes everything from the game's connection to its four-color roots to the latest changes in the game's mechanics.