Before I get to the meat of this suggestion;
Simply put, the Workshop should not be tied to Housing, given the limited supply of plots. Instead, a corner of the three starting cities should have an entrance to the Workshop that any Free Company can purchase access to, with the existing Housing version simply being a "shortcut" to the same instance.
Furthermore, I think the Aetherial Wheel should be removed as furniture in its current function, and instead moved to the Workshop, with the existing Workshop recipe changed to function as an upgrading system to this new version of the Wheel. The old version could perhaps remain as a simple furnishing, but once again, the utility it provides (Grade 3 Free Company Actions) should not be gated behind owning an estate.
Not a Housing "fix", but it would sure take a lot of the heartache out of not being able to get a plot, which is a reality for a lot of Free Companies, given how pants the whole Housing system is handled.
Now that that's out the way;
Rework the Airship/Submersible system. I honestly think this could provide some fun additional Exploratory Mission style content to the game, that is Free Company based. Something akin to Treasure Maps perhaps, just a bit bigger in scale and based around Free Companies (you know, those things that have no purpose).
First of all, add Boats to the mix as well. You build a Boat, then an Airship, then a Submarine. Classic Final Fantasy vehicle progression.
Second of all, add a new function to the Retainer Venture aspect of sending these things off, so that when they return you have a chance to gather your Free Company together and enter an instance for additional rewards. Random chance to gain access to that instance, maybe based off the ships stats, rewards could dip from the same pool as the Ship Ventures themselves perhaps, just in greater volume since you'd be doing actual content for them this time.
These instances would be based on what you sent out of course, Airships would have you exploring Diadem style floating islands, Submarines could have some underwater bubbles/caves, maybe even some sunken ruins, etc. Boats would naturally take you to some uncharted (?) islands, you could even have anomalies at Sea which result in a special boss fight with you fighting on the Boat vs say a Kraken. Could do all sorts of interesting things with it TBH.
Objective wise for islands/caves, you could do a number of different things, though I would first have a reason to split the group into two. One stays and defends the vessel from waves of enemies, with the ship taking damage if they fail, eventually resulting a a wipe (plus ship parts requiring extra repairs). The other would be the "exploration" group, which has the goal of finding the "treasure" and bringing it back to the ship. You could vary the types of encounters both groups face, a basic idea would just be to copy FATE design, mob waves, boss FATEs, collect X to ward off enemies, etc. with it up to your group to access the encounter and decide how many people to send out and how many to defend. Perhaps your exploration group wipes, so someone from the defense group goes out to raise them? Could do plenty of interesting things with this I feel.
TL'DR; Have you seen Sea of Thieves? Basically that, but good. I think that would be fun, something like Treasure Maps, just a bit more involved and interesting off the back of Free Company Ships.
Again though, to reiterate my first point; You cannot add something like this while the Workshop is limited behind Housing. It just doesn't make sense to make something interesting like this when it's locked behind something only a finite number of groups can access - certainly not why Diadem failed the first time, but there was certainly a lot of complaints about the Free Company specific version of Diadem back when it was originally launched, precisely because of this issue. Building and having a group Airship should be something cool and exciting, but it's not... It's just an additional Retainer Venture... If you'd told me 10 years ago that I'd be able to build and own an Airship in a Final Fantasy MMO? I'd have been so damn excited. I'm not though, and I don't think anyone is, and not because the majority can't access the content, but because Ship Ventures are lame af... Please fix... Make it fun, interesting content, that justifies the existence of Free Companies...