I haven't found towns have had the same effect since the series moved to full 3D.

I agree with you about the shops, but I think you understate the importance of shops. One of the biggest joys I have in a game is finally reaching a new town in a far off local and running around to all the shops to find out what cool swag they have.

Also is the sense of safe haven. Back in the old days your MP didn't restore automatically at save points. Towns meant places to rest from your previous adventures and prepare for your next escapade. As they have taken virtually all of the sense of danger out of dungeon exploration naturally the sense of relief at finding a town is seriously diminished.