Well i am personally a pilot/slash gunner so i love the flying aspect of the game. Yet i do want some challenge in the mix so i think there should be some restrictions put on if they do implement it.
For instance i would love to have a overheating/cooldown feature so i know i must use my bullets wisely. Also i would wish to have atleast a few payloads but they would take forever to reload or i would have to purchase them as mentioned before.
For the armor i would like to be bulky and strong yet slow. Or light armored and agiled. Now i personally think the pilot in his cockpit should have a better chance of survival than say about 5 grunts or else getting into this vehicle would be pointless. Yet i dont want a super powered fleet coming up on my ass.
Now also i dont think a ship should be handed to you as easily as a gun. I personally it should be a high level quest or you would have to meet the nsspecifications or something or another. I personally liked how they did transportation in the game MU also made by Webzen. Those are hard to find and rare yet effective. So when you saw someone with a horse or whatever you knew they were good or atleast waited long enough for one.

Thanks for listening,
Your future friendly pilot SolidSnake-Alp