I know the team planned to let us join only one company, and I can see the value of making a choice, but honestly I think the game, at the moment, needs to make every little piece of content available to every player. It's not like we have too much to begin with.

Maybe let people chose a "primary" company, and give them the ability to join the other two as "guests" or something similar, allowing them to still rank up as normal (doing all the quests and enjoying cutscenes and such), but limiting their access to some of the rewards that should be given only by the primary company. For instance chocobos and such.

This will also avoid people chosing a company according to the rewards, resulting in companies only by players that have favored classes compatible with the rewards given (for instance as it stands now every gladiator would join the Ul'dah company).