That's true - creating an atmosphere requires some effort and time whether it's high end 3D or oldschool 8-bit style icons.
After reading this article, it became clear to me that players do want bases. After all, for most of them players character is nothing but a doll they control, and, for them, the more control they have, the better. That's why all these anime games are so popular nowadays - they allow players to do as they please. After all, we can't ignore the fact that bases do their job of bringing players to the games.
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Remember an RPG is about telling a story and story should have a meaning. Think about all the greatest movies and books, they have some kind of underlining message that permeates them.
Visually I think it's the artists job to incorporate the message of that game into the graphics. This is very similar to film techniques that you probably learned about in high school. Like how some scenes in the Matrix were shot using a green filter, to signal to the viewer that something wasn't right, that perhaps this is illusionary or digital.
The same should be said about the RPG. The way you use color, lighting and detail should reflect your underlying message.