I personally hated the Flying Fortresses myself. They seemed to be mostly a waste of time. I gained probably 3 levels total in them, and I finished a few sets, but besides that it just seemed like I was getting more annoyed than having fun because of the amount of enemies. It's not that they are hard on their own, but as my thread about Homing Arrows says, when you have an entire wall of archers shooting at you with Stun Arrows, it gets extremely annoying very fast.
When I got to the third FF, I just found the chests, took them, and flew away as fast as I could because I didn't want to deal with it at all.
So far, though, in FoV, the EXP gain is pretty decent. I'm I think 40 or 41 and I still get a decent amount of Experience a kill on monsters 3-4 levels under me.
I almost don't want to play the game on Hard simply because the monsters themselves seem to use a Quantity over Quality guideline, which is annoying when you have no party.
I would love to play the game again, though there are little tiny things throughout that bug me. Not to say that the game isn't great, it still is probably the best RPG I've played in a LONG time, it just has it's own little quirks that bothers me. Every game has them, however, so it's not a big deal.