I remember when I first reached Mor Dhona in ARR, it honestly felt like *THE* end-game hub I'd been waiting for! I loved the music, the place seemed brimming with life, the PERFECT location to launch out on a new adventure! When the Scions moved there, I couldn't have been more excited.
Honestly though, I feel like the zone could use a little love. It just has SO much atmosphere -- it reminds me a lot of Hollow Bastion/Radiant Garden from the Kingdom Hearts games, actually -- and to me, REALLY made FFXIV feel like a proper "Final Fantasy" world.
I honestly have a couple of different suggestions for the place...
1. Making it a "new starting area". Let's face it; the story is still incredible, but there's a bit of a steep investment of time for new players. I might suggest having this as a new area -- perhaps alongside whatever new job(s) might appear next in the game -- and have it tell a slightly expedited story (as compared to the other areas). As in, removing some of the "filler" quests, which could remain in-game but optional in those areas (or even allowing us to experience EACH starting area and story via New Game+).
Alternatively, it might just make a great starting-area for the game in general (maybe DURING the opening levels, it reverts back to the base-camp it was originally in ARR), and you could revamp/remove the "Class" systems, simply giving you the Job Crystals of your choice, and sending you on your way around level 5-10.
Oh, and maybe your "first scion interaction" could either be Urianger, or perhaps a G'raha Tia urging you to reach out to his "fellow Students of Baldesion", leading to your introduction to the Scions?
2. Perhaps adding a new quest-series to clean-up the zone? Removing Imperial structures, maybe doing something a little less dreadful-looking with Midgardsomr's corpse, perhaps even building it out into a castle of some of sort? Or maybe Midgardsomr decides to entrust the fate of his kin to you, his body dispersing into aether, freeing us up for the "clean-up crew"?
Might also make a cool area for a future housing settlement... (although, I would love to see the city there maybe get more steampunk-ish buildings, or perhaps floating isles?)
3. I honestly wouldn't mind seeing them resurrect the Crystal Braves, as the "grand company" of Mor Dhona. Admittedly, your GC choice REALLY doesn't matter -- even in PvP, the game just throws you in whichever team(s) need bodies -- but thematically, it would be cool to see that once-tainted idea finally come to fruition. Maybe an optional quest requiring you to reach "Champion" rank with all three GC's (which, PLEASE open those up for us anyways, Devs!), allowing you to build them up and become "Crystal Champion"?
Just my thinking, anyways!