I really enjoyed going to MOS Burger, but found that some locations were MUCH better than others.
Downtown Kyoto, and Akihabara, Tokyo were the best two locations for me. Both used real glass for their drinks and had all the special touches that made MOS Burger such a special place. Akihabara even gave out rubberized coasters for your drinks.
I also went to a MOS Burger in a subway mall in Osaka, and it wasn't nearly as good -- plastic cups, food was immediately given to me and it was kind of a typical small fast food restaurant.
Also, I thought the "fresh burger" was the best burger on the menu. I really appreciated that the burger was small enough that I had enough room for dessert ... a macha ice cream sundae with mochi balls.