Side balancing is a good idea for a game, but how to go about it in THIS game is a bit of a problem.
You can't force players to a side. to many players and this includes non squad attached players are too team loyal. HTC has proven time after time that they don't like to "force" anything. They prefer to let the kiddies play.
Side switching I think could be adjusted. I don't know the "why" HTC have kept it at the 12 hour rule. Maybe it's for spies, maybe it's to stop wild swings in ENY, maybe it's curb the jumpers who don't know about win the war requirements. I don't see where a 4 hour rule could hurt, and it certainly would help those that want to jump looking for fights.
ENY, you can't make it act faster or do any other over all adjustments to it because it would effect the whole map. So if it kicked in harder it would be possible for a team to be hording on one front with an ENY restriction, at the same time trying to defend on the other front against a horde with that same ENY restriction. Zone ENY would help with that, but how much trouble would it be to implement? Would it cause the reworking of all the maps? Only HTC knows.
Better organization would help, but it is a game after all and while some players do seem to spend a lot of time playing a "Supreme Command" would have to be on all the time to keep the teams pointed in one direction. While there are a lot of people who couldn't care less about the "war" aspect of the game, those battles are what drives the action the "furballers" look for.
Side balancing is not an easy fix by any means.