what I would like for shops is that I won't feel like I'm the only one that actually shops there. Show me some people browsing the wares! I don't mind the pop-up or the feeling as if 'I'm buying out of his/her pants' but I would like to see some customers looking around, contemplating what they are going to buy. It would make me feel as if I'm not the only thing keeping the poor guys business afloat.
That part worked well enough in Oblivion and Fallout, it was other people in shops, might want more people and some shop related dialogue.
Primary wish is a shopping chart like in Fallout 3, it made buying and selling stuff easy and you did not need to confirm buying a single apple, and show total weight in the shopping window, so fun buying a set of armor and be unable to carry it, press a button to sell a stack.
3d view of objects is inn and sounds nice, I do not want a fancy or realistic system I want something effective, we will use a lots of time buying and selling junk so having to haggle for each item would be boring very fast.