Store owners will slowly come back, and the shops will open eventually. You can speed this up by contributing to the kingdom's treasury. I have also worked on improving the kingdom cities' individual economies. I'm not sure if this has been confirmed or not as to bringing shops and such back quicker, but it definitely worked in Fable II, and I assume it does in Fable III.
I started working on the Magnate Personality achievement, buying up houses that were vacant and renting them out to what townspeople still were. I repaired them, bought stores, etc., but that depends on how much money you have. Of course, renting more means gaining more, but you have to pay up first to do so. I also started carrying out relationship quests to befriend the people; a lot of them were angry with me in the aftermath, it's the way to the Popularity Contest achievement, and it gives you guild seals if you haven't finished unlocking all the Road to Rule chests. Basically, there's a lot of achievements that you may have not completed yet if you stuck mainly to the main storyline beforehand. Some will pass the time more than anything, and others are pretty fun, like the Henry VIII achievement. There are also quite a few side quests up for completing also.
Is there anything you're particularly needing? At the beginning you have to scavenge for most things, but I might be able to point you in the right direction.
