Just a out-of-the-blue idea i came up with. Just thinking that if someone wants to change their allegiance, they should have at least all of the quests done from each company up to the point where they can choose a single company. This way, say a player wants to change allegiance, they can start at that initiate Company Rank. Upon switching back, they start over at that Initiate Rank all over again.

The price of changing Allegiance would be to hand over all of your current credits for that Company.

However, I am sure people will abuse this system in some way or another by getting the higher rank items and selling them, so perhaps the Companies should have their own rare/ex versions of items like some that are already listed. With this system implemented, players wont necessarily feel locked down to one company, but would have to spend vast amounts of time working towards collecting the best items from each of the Grand Companies.

Also, upon changing companies, you lose your chocobo. lololol