I would agree that most JRPGs cities are frauds. But I like it this way.
I am not a fan of immense town with hundreds of NPCs to speak with, dozens of place to visit etc...
I like to visit so cities but it has to be rather short to do. Otherwise it usually feels like a waste of time for me.
Now that I think about it, from recent memories (played it last year), one of the only time I enjoyed a big city was Baldur's Gate (but not JRPG).