How hard would it be to try out an expansion where zones aren't locked by MSQ,
-not saying yay or nay on this, but what purpose would it serve? I'm not being dismissive, I'm honestly curious.

-where quests don't have braindead markers telling you where to go
And 96% of people would hate it and look it up on Google, anyway. Put in a toggle that turns them off for the masochists that want to do that. I've done my stint of 90's-early 00's MMO quest design. I'm done with it.

-where dungeons are nothing like the stale formula we have
So what, like branching paths? "Proper" dungeons, maybe? Problem with that is that 96% of people will find the most efficient means of completing a dungeon, and always do it that way. Any deviation from the norm will not be tolerated.
Just like something like skill trees, the developers might intend there to be choice, but the community will dictate and enforce the choice for you.

-where underwater isn't just a pretty landscape and combat/breathing mechanics are tried out.
There has never been a MMO, and very few games (if any) that have done underwater combat well. I do not think that FFXIV would be the one to break the trend. And if they did try it, and it sucks, it'll just be another "Meeeeeh, why'd they waste resources on that" situation.

-Where exploration and open world events are tried through the entire introduced zones instead of designated exploration instances like Eureka and Bozja.
Rather keep them seperate, thanks. Last thing I want to do during MSQ is to have a bunch of mobs eating my ass just because I had the audacity to want to go from point A to point B. Again, did my time in old MMOs. I'm done with it.

-Where some side quests are just damn hard
Sidequests? So purely optional? Sure.

-Where some open world dungeons are introduced, and the mobs are just lethal
I can't think of any instance where open world dungeons are implemented where it isn't just a big free for all flustercluck. It's all fun and games until you and 20 other groups are all camping the same boss. Especially if that boss has an absurd respawn timer.

Sounds like you just want an old school circa 90's-early 00's MMO. Fortunately, there are many of those still in service that you can try. If you're looking for this game to become those games, though, don't hold your breath. There is a reason why most of these old MMO mechanics have been regulated to the dustbin of history.