In the .dat files wasnt there a bit of information about a guild being located in Ishguard, that would pretty much quash your dungeon/raid theory. Never played FFXI so can't comment on what Jeuno was but I would think Ishguard is going to be a larger more advanced version of the current city states. I think you might be right about the chocobo's/airships, I also think Ishguard might have something to do with Hamlet defense battles too. Hopefully we might get some more info as the weeks pass.