I like stealing as it is in the game currently. Maybe minor things like merchant prices or people having a lower opinion of you because you seem shady are okay. But putting too much restriction on it will then turn some people off from stealing entirely. I wouldn't want to feel like I have to play a certain way. For those who don't want to steal you won't. For those of us that do want to steal we will. If the NPC's will start to associate their missing things with me, then I should be able to Charm/Reason/Intimidate my way out of the situation. Also any negative factor should have a way to offset it as well. So merchant prices are now higher? I should be able to put points into some stat/trait to bring it back to normal. Same with opinion. So this way if I want to be a thief I would be a charismatic, silver-tongued one.
Yeah, I have no problems with stealing being effective if players are willing to commit (points) to that role. Heavy point investments placed in sneaking, lockpicking and pickpocketing should allow you to get away with these acts without getting caught. However, even though a character doesn't get caught, NPCs should be smart enough to realize the town is being cleaned out after a certain someone (the player) showed up. Investing heavily in social skills should be required to help offset the consequences of that.