Bethesda has always had this problem creating a proper use for money. The only real reasons to use money are houses, training and the achievement.
So I suggest the following:
1. Stores have usefull stuff. Why alchemy stores never store River betty or human flesh? I need those and I'm filling to pay. Why can't stores sell deadric arrows on lvl 1? Just make them expensive but not too expensive and in large enough quantities (ie 100 steel arrows, 50 orc, 10 deadric).
2. Unique stuff for stores. Remember how in oblivion stores had custom items for sale but they were usually expensive (and when you got money to buy them they were crap). So why can't solitude fletcher have some awesome bow with some unique enchantment that you can't replicate via enchanting. Different shop might have different unique items (alchemist store some super potion or poison, smiths might have armor or swords).
3. More training. Not everyone wants to level alteration to get max level so WHY the frigging training limit is 5 per level? I use mod that allows me to train 20 times per level. The cost alone keeps me from power leveling too much.
4. Stores could provide services. Smiths could improve your armor, priests could provide some long term blessing etc.
