Do you know how heart-poundingly suspenseful it would be to stand around in a virtual store for hours just to catch a rare glimpse of someone actually ENTERING YOUR STORE!? SO EXCITING!
Player owned stores would be fine, but the player being the shopkeeper would just be ridiculous. Hire an employee. The game keeps track of your relationships, maybe you can hire a friend. The more they like you, the more willing they are to take the job and the lower the pay they are willing to work for (although if you keep their pay to their lowest tolerable amount, then they will start to like you less). Higher mercantile employees bring in more money, but they cost more. Sacking employees hurts your relationship with them.
I did mean you would be able to hire someone, just forgot to mention that.
The thieve even t would only be if you're there, as there should probably be an option to tell your employee they're off early and you'll take over so if you ever do feel like running it yourself.
I agree on the rare NPC problem- shops in games where NPCs are rarely seen, for lack of a better term, svck.
Maybe if no NPC's are walking by, one randomly generated just labeled as "customer" comes in.
Of course, better positioned shops with more people walking by would cost more to keep your gold down, at least for the time being.
Maybe if you have one on a road, you could have bandit or daedra break ins, or who knows, maybe even a dragon start a wall on fire.