Here's a simple solution and it's three words: "Rural Airship Travel"

Basically what needs to be done is airship travel should/needs to be expanded to areas outside the main cities. If you look around some areas they already have large structures that resemble airship docking platforms. Add in travel to these locations and it'll solve a good deal of needing to be reliant on anima to get to exclusive areas. Not to mention it'll promote usage of the airships and help deflate gil from the economy.

An easy way to do it is position an NPC near each docking platform. You pay a fee and it teleports onto the top of the platform. A cutscene will play after a short while showing the airship docking, you climb aboard and get returned to the nearest city. The airships run to and from the outlying areas every 5-10 minutes and cost maybe a third more than travel from city-to-city.