Right now, a hidden village only exists for quest locations and to fit with the Naruto story, they have no other use than this (except for konoha). I think the hidden villages should all have everyday ninja facilities (i.e food shops, weapon shops, dojos, clothing shops, etc) with some different facilities exclusive to certain villages so that they actually have some amount of practicality. This would probably alter some of the game mechanics (such as hunger) but it would also help to bring a more life-like experience (especially if the buildings looked a little nicer).
Most things were centralized in the Hidden Leaf because we didn’t have the other villages built and were focusing on other projects as the server grew. It was sort of the hotspot for the five years the server has been up. The goal is to just push more mission locations and possibly clones of the existing jutsu and weapon shops into the other villages. Creating exclusivity would only be practical through the weapon and jutsu shop, and with that would come difficulties in balance.
I don’t think I want to alter the game mechanics to add hunger. Hunger messes with saturation and healing. While the experience is meant to be immersive, your suggestions seem to lean heavily on roleplay and our server is based around PvP.