I see a lot of talk about balancing out 1v1 or even ManyvMany as far as events, encounters and war. I haven't seen any discussion regarding alignment imbalances on a server wide basis.
It has been a problem in other games when one side has a slight advantage in numbers and/or skill, the server starts getting a reputation for being a Side A server. While another server is Side B and so on. Pretty soon, PvP is no fun because if you are Side B on a side A server, you get facerolled. So, if you want to play Side B, you go join a Side B server. The end result is The Side A server has horrible PvP because Side B is never around and likewise for the Side B players on the Side B server.
Now I realize in PFO you are not choosing Horde or Alliance, Light Side or Dark Side, but there will still be choices in regards to how you play your alignment. If the Evil ones become dominant or the Do-Gooders control the server it won't be balanced and it won't be fun for the weaker side.
So how is the risk of alignment imbalance server wide going to be mitigated? I am no EVE expert but I played a bit. There are warring factions, corps, etc; there are those who smuggle/deal in contraband but the races and sides were never mapped out as EVIL vs GOOD like they will be in PFO. You can play an aggressive, player-killing style in EVE but no race has its explicit purpose to be acts of evil. Horde were supposed to kill Alliance and vice versa. Sith were supposed to kill Jedi. Heroes were supposed to battle Villians and in PFO Evil will be pitted against Good. But in EVE, the landscape is much more gray so I think PFO players will respond more like WoW, SWTOR and others that make it black and white. I think this will also lead to the server imbalances that affect other games.
PvP on a balanced server is a ton of fun. But an imbalanced server sucks all of the fun out of it for me (and most). For anyone who says this game is inherently different or that the player behavior will be different, I think you are being unrealistic. Gamers will seek every advantage they can get and exploit every opportunity possible. You cannot predict how players will respond.
Some will say they love the challenge of being outnumbered - well, you are not the norm and do not represent the majority of gamers. Some may suggests players will auto-balance themselves to make the game more fun - some may, but not most and not enough to make a difference. The only behavior you can be sure of is that gamers will seek and take any advantage they can find.
There will be moments in the game where players can play Evil with great benefit due to a "loophole" or unintended consequence of the game rules. When that happens, players will flock to that gamestyle. Some other time, the Good players will experience some boon and players will herd to that style. It happens in every game, every time. Having characters who are inherently pitted against one another will always create this problem. I think this is a huge potential issue that vastly outweighs balancing on an individual encounter basis.
As players, we must be prepared for this. It will be frustrating and sometimes head-banging against the desk worthy. Its going to happen so don't get crazy with anger when it happens. Even if the designers put a system in place, it will be flawed so when you are playing in the Beta and the incentives and disincentives don't properly adjust the behavior, do not Rage.
I know I'll get crushed for saying this, but one answer is to do away with Alignment as a label. There are no classes in PFO afterall that you label yourself. Why label yourself as an alignment? Your actions will determine if you are good or evil - why is there a label? Just like your actions guide what class you are - there is no label. If you click on another player it won't tell you what class they are in PFO.
The benefit is that players will fight for their own and their company's benefit. Not because they are "supposed" to be Evil or "supposed" to be good. Sometimes they may choose a less savory path and others will take the high road, but at the end of the day they fight out of a pure motivation - not a trumped up one based on a label in the game.