I wouldn't mind at all if the FE's were episodic like the new story mission setup is, but I don't see why they're tied into the natural progression. Seems like an odd choice to me.
This is probably my biggest objection to them including the FEs into the mission chain. I can understand (to some degree) them level-banding them, but I've always felt they worked well as optional side-stories, little interludes in the larger plot. The mission pre-requisite as a whole is something I think needs to be rethought, but that may be for another thread.