I hope the following questions will be answered or made clear soon:
1. Can I as character from Ul'dah still join The Maelstrom?
2. Are their benefits for DoL to be a botanist in The Order of the Twin Adder or a miner in the Immortal Flames?
3. And will it also change quest content and possible other future content for my character, if yes how much?
4. Is the company of your choice a permanent decision?
5. What will the role of companies be against the Garlean Empire and are there notable differences in the roles of the companies?
6. Will the companies equally affect the gameplay and content of the DoH and DoL aside from the DoW and DoM?

Personally I would like the choice of company to be a permanent decision since it could lead to a bit more diversity in players.
I really hope the questions I have above can be (partially) answered or made clear in the near future.