Caution: Minor Spoilers for Skies of Arcadia and Phantasy Star IV
I'm going to tell a little story now. This story involves three characters named Vyse, Aika, and Fina. Many readers will recognize these names, and I choose them because the game they star in happens to be one that I have played four times and enjoyed greatly on each of those occasions. To any readers who do not recognize the names, just keep reading. And yes, this would count as a very mild spoiler for the game in question.
While on the deck of the Delphinus, Aika spots a herd of Loopers in the air. She grumbles a bit and strides inside the ship, closing the door behind her. Fina is inside the doorway and they converse briefly.
Fina: Aika, what keeps drawing these poor creatures toward us? Is this ship too noisy?
Aika: Gosh, I don't know. Maybe they're just bored. I'm not very happy at how they just ruined my cloud watching, though!
Fina: Well, there's no reason to bother Vyse over this. We'll just keep the doors closed and let them fly away.
Aika: Sounds good to me. I think I'll take a nap; it's not as if we've never done this before.
Fina: Shall I get a cannon ready to fire, just in case they block the windows again?
Aika: That'd wake me up! Just let them get bored and blow off the window, we know to stop when the icicles start talking to us.
Vyse: I don't think letting you take a nap and dream up more nutty things in Glacia is going to help.
This exchange invented by me is what would result had Vyse's ship, the Delphinus, been recognized for what it is: a gigantic weapons platform that is self-sufficient in the air. Its occupants certainly have no need to rush out onto its deck in order to engage a host of creatures that will either get bored and go away, or blow off the moving ship. For whatever reason this is not how events proceed, and instead an all-too-frequent event in Skies of Arcadia is something like the following:
Aika runs to Vyse and Fina breathlessly, carrying momentous news. Both look at her with resignation, as they are already tired from their constant exertions. The Delphinus's engines are wearing out from constant stops in its transit.
Aika: I know we just cleaned the deck from that last batch of creatures, but more just showed up and they look mean!
Vyse: What is this, the tenth time today? Doesn't matter, I can't allow ugly monsters to be temporary hood ornaments on this ship! Let's run out there and boot them off!
Fina: Cupil, I hope you're not getting tired of transformations. Those monsters are very bothersome.
I chose Skies of Arcadia as my lengthy example here of the phenomenon under discussion because it does so many things well, and still manages to treat the airship without the respect it deserves. As seen in the ship-to-ship battles, airships in Skies of Arcadia possess cannons. Why these cannons cannot be used to simply blow the bothersome baddies off the bow I do not understand. The cannons are unnecessary anyway when enemies can only bring an airship down by smothering it with their bodies in the hopes of clogging its engines (as seen in a neat battle in Sakura Taisen 2 or making it weigh so much that the ship crashes.
While not an airship per se, the Land Rover in Phantasy Star IV offers an excellent example of how to use a party's transport for something unique. In transiting the lands of Motavia via the Land Rover, which is exactly what it sounds like, the party will encounter enemies. These enemies are, however, unique to the Land Rover, and instead of party members getting out onto the deck to fight the Land Rover itself does the fighting, with its own HP and unique heavy artillery to blast the opposition. The Ice Digger has a similar mechanic on Motavia, with unique enemies being engaged by the transport instead of the party. Phantasy Star IV still stands as the only game I have played to use this mechanic, and it is now 15 years old.
Airships are used for transport in RPGs, with barely any exceptions. For those titles that do incorporate combat on the airship, why would the party want to engage in the same style of battles they do on the ground when they occupy a gigantic flying weapons platform? I cited Phantasy Star IV's innovative use of transport in combat, but the only other example I can think of is Final Fantasy III's final airship using Fire Support against random encounters in the sky. Many games nowadays eschew a world map and simply have the party shuttle from place to place automatically, but those titles that do use an airship should try to work it a little more into the battle system.