Stores in Cyrodiil
I guess in a round about way this whole topic is about shopping. The devs have made some important changes in the way that stores operate. In a lot of ways, these changes represent compromises between the way that Daggerfall and Morrowind handled commerce. Some of the more notable ones:
Like you, merchants have a Mercantile skill and most of them are probably going to be better at it than you, at least at the beginning of the game. But the way that you get better is to haggle over the price. So when you open the trade dialog, click the "Haggle" button and mess with the slider. The farther to the right you move it, the more gold you're going to get for your sales and the less you will pay for your purchases. But there is a point, beyond which the merchant will not buy/sell. This point is a combination of the difference between your Mercantile skill and the merchant's as well as the merchant's disposition toward you. Without getting into the algorithm (which I don't know), the short answer is that you'll get better prices from merchants who like you than from merchants who don't like you.
So the trick is to find that point without losing disposition in the process (merchant disposition drops one point for each offer they refuse). Conversely, when you make a transaction, the merchant's disposition increases (the bigger the purchase, the bigger the increase). What I have found to be workable is to buy or sell cheap stuff, one item at a time, and bump up the Haggle slider one or two clicks before each transaction until I find the point where the merchant refuses the offer, then back it off a click. The game remembers where you set the Haggle slider for each merchant, so you won't need to be haggling over every transaction when you return. At that point, I can go ahead and sell the more expensive items. This lets me get the most gold for my loot, while gaining the maximum possible increase in the merchant's disposition at the same time. After several large transations, you'll find that the merchant's disposition is 100% and you can go back to bumping up the slider a click at a time until you hit his maximum ceiling again.
While you are still Novice level in Mercantile, the price you receive for an item will drop if it is not in 100% pristine condition. If you want to maximize your gains, repair everything before you try to sell it (which will also boost your Armorer skill). Sometimes it may seem like a bit of a waste (why blow 15 or 20 gold for a hammer to use on an item that's only worth 5 or 10 gold to begin with?), but the Endurance multipliers that you'll get for following this advice will pay off handsomely in the long run.
Once a merchant's slider is set, you won't need to mess with it unless your Personality, your Mercantile skill and/or the merchant's disposition changes. If any or all of those three change, you'll need to change the slider to maximize your sales. And for those of you with low Personalities or low Mercantile scores, don't underestimate the power of potions, ingredients (Imp Gall, for instance) and spells to increase merchant disposition. Remember that time stops while you're in conversation, so all you need is something that will last long enough to start the merchant conversation and the effect will last until you end it.
Another change is merchant inventory. Aside from a few near-certainties, any given merchant's inventory is handled pretty much like leveled loot: it changes depending on your level and other random factors. A merchant who has a particular item in stock on one day may not have that item the next. This is supposed to be a reflection of the local NPCs picking up items that match their goals and objectives, so if something isn't there the next time that you come in, someone must have "bought" it. There are a few items that you can pretty much count on, though. For example, smiths should always have Repair Hammers, Alchemists should always have at least some alchemical equipment, dealers in enchanted items will almost always have soul gems, etc. And many merchants carry a "specialty" item. This would be, for example, an enchanted piece of armor that merchant, and only that merchant, carries. They are all on the pricey side and some of them fall into the cheesy category, but they are there if you feel like indulging.
Remember, that once you hit Expert in Mercantile, you can pony up 500 golds to increase the merchant's price cap. You'll make that money back several times over if you limit yourself to investing in shops that have decent starting caps and low merchant Mercantile skills. And once you are a Master of Mercantile, all merchants have an extra 500 golds.