The Inn thing has always been one of the most blaringly obvious forms of this Story (World) and Gameplay Segregation, because you don't even have the alabi of having different shops with different items/equipment. How do the people in this town afford 6,000 Gold to sleep a night in a little log cabin, when the early-game work I did paid 300 Gold (which was more than enough to cover the 30 Gold to sleep in a nice inn there)?!
It's even more annoying because often, the player can inconvenience themselves to travel back to an earlier town to not have to pay the exorbitant rate!
Of the four games I've completed in RPG Maker, 3 have been - by design - in game worlds of limited scope where the player could visit any location at almost any time (and therefore it made sense for prices to be even everywhere), and 1 eschews money in favor of "credits" you earn for shops by accomplishing local missions (therefore limiting the absolute number of things you can buy in a given location). Thus, so far I haven't actually tested out my "economy design" in a standard, epic kind of RPG.
But what I plan to do when I create an epic RPG with a big world is to not scale the amount of money the player gains from combat/treasure chests/quests/etc. as they get further in the game. Experience and certain other rewards will scale so that the ideal solution isn't "grind weak monsters from early levels forever because they're quicker and easier than the ones you're supposed to be fighting", but money won't scale. Therefore, the price of an early-game stay at the Inn will be the same price as a late-game stay. The price of a Potion that cures 25% of your HP will be (approximately) the same in the first town as the last town, and your money - rather than your distance from the final boss - will be what gates you from buying that Sword of Supreme Slaying in the second town an hour into the game. There will certainly be some challenges I'll have to get past, but the idea is that this not only creates a much more realistic economy and a more believable world, but also allows me as the designer to open up a lot of new freedoms to the player without gating them behind "how far into the game are you", and additionally creates some rewards for engaging in combat against earlier monsters (something I've always enjoyed doing in some of my favorite games).
I think another interesting way to handle it could be to have all inns/stores/services increase their prices as you complete more of the game (and therefore have access to the monsters/treasures/etc. that pay much higher). No one even stocks Potions any more - you can only buy Hi-Potions now! And all the Inns are charging 2000 Gold for a night's stay! This wouldn't be realistic and the best you could do is hand-wave it, but I think it would actually serve the gameplay very well.