First of all, I don't see the problem. Airships are useful and fun as is. Right now, they're just a tool for a very small number of FC members to play with, but which the whole FC can help make. Airships themselves aren't a waste of time or money - they're the only way to get level 3 company actions, and they can also bring back level 2 ones along the way (including one I think isn't available by other means (Jackpot)). They also bring back a few unique items, such as toyboxes and iron dwarfs, though those will lose their value quickly as more people get their airships leveled. But the grade 3 and 4 materia they can bring back in large quantities? That'll be useful for a while.
The problem with airships as they currently are isn't that they aren't worth it or that they don't involve everyone in making them (they can but don't have to), the problem is that not everyone gets to see them or do anything with them. That's what 3.1 is intended to resolve - letting everyone in the FC who worked to make the airship parts able to see and utilize the airship in some way. If this means that, for the purposes of the hidden islands, the airships are just mount glamours, that's okay. It still serves the necessary purpose.
If the only reason your FC bought a house, built a workshop, made airship parts, and leveled your airships was so you could make money from hidden islands, well, you're doing it wrong. Those things are supposed to be fun, and they're supposed to give other benefits not available otherwise, which they do.
Now, all that said, what would I like to distinguish FC airships from rental ones? PvP. I'd love to see airship battles as a PvP minigame involving a light party, full party, or alliance (don't care which). Is something like that needed? Heck no. Would it be fun to don an eyepatch, get out the parrot minion, and start shouting terrible [sky]pirate-speak while firing cannons at an enemy [sky]ship? Heck yeah!