Paul banner balance has been a pretty big issue since it was implemented. I'm not going to list all the pro's and con's here, but it allows for factions to "pub stomp" http://www.urbandictionary.com/define.php?term=pubstomp
It's a big reason why people complained about archers or horse archers/xbows (because there would only be 5 horse xbows in game, and they all had the same banner, so they were all on the same team). Which I believe the banner balance system has influenced a lot of the nerfs that have happened over the years. I don't care if it's class balance that's implemented, but it shouldn't be solely based on banner balance (or mainly based). The balance system has been borked since it was implemented, it's been discussed ad nauseum, and I really don't want to drum up all the arguments this early in the morning (for no real reason anyways, as you say it wasn't changed for a reason).
IMO the balance system should be weighted (from top to bottom) something like this (with banner balance being the ultimate goal, but not at the expense of these variables):
character level
class/equipment equipped
K:D of last 5 or 10 maps
And if it can make fair teams with those variables and still allow people of the same banner to play on the same team, great. But I don't think those variables should be put aside just so people with the same banner can play on the same team. Relatively fair teams should be more important in public servers.
Ban all ranged.
Says a dedicated thrower.