Cavalary: I'll first tackle Mortius1's post and say that being unable to sell everything at a normal value is awfully frustrating, and that also includes option 3 from there. But I think there's one more option to include, the barter system, like in Gothic, so the store may at times have less money than you'd like, but will have other stuff you can nevertheless trade for.
That restriction is one thing that annoyed me about Avernum: Escape from the Pit; all stores only give something like a paltry 20% of the price of an item. This is one of the reasons I decided not to play it and instead play Avernum 1, where some stores sell for a decent value.
50% of the price is the typical standard amount of money you get for selling an item; some JRPGs actually give you more (Dragon Quest 2 is an example IIRC, as, I believe, is Dragon Quest 3), but I'm not aware of any offhand that give you less. WRPGs, however, have cases where you get almost nothing from selling an item. (On toe other hand, the one RPG I'm aware of where sell price = buy price, Ultima 3, would be classified as a WRPG, unless one considers that what I call a proto-RPG.)
The barter system is precisely how Morrowind operates. Merchants have limited money, but you can buy and sell in a single transaction, even if the amount you'd get for selling alone would exceed the amount of money the merchant has. Hence, even if the merchant can't afford your filled soul gem on its own, you can pick up some items the merchant has in the same transaction and not have to pay extra for them.
Incidentally, there's one other game I can think of that does buying and selling in a single transaction; Star Ocean 2 (PSX JRPG). While this usually doesn't matter, the game actually has one item that sells for a negative amount; the Bounced Check, which is obtained by using a skill that is used to do things like forge documents and failing. If selling would put you into the negatives, the game actually won't let you sell it. (That game doesn't limit merchant funds, so it doesn't lead to bartering being necessary.)
Lennus 2, which I'm playing right now, seems to offer 60% of the price when selling items, and there's a mercenary you can recruit who reduces purchase prices to 75% (which is huge when there are powerful, but expensive, items available early in the game). The catch is that that particular mercenary, whose recruitment fee is -500 gold (in other words, he pays to join your party), won't leave your party if you try to dismiss him, and he isn't good in combat. (He only leaves if he has 0 HP at the end of a battle.)
Cavalary: Past that, out of the 3 purchase options in the OP, 3 is the most annoying. Level scaling in anything is an awful design choice, and in this aspect on the one hand doesn't allow you to jump ahead and on the other just adds one more aspect of the world that appears to just revolve around the PC, which breaks immersion.
How would you feel if the game has a Mercantile skill (or similar) that you can improve in some way (like with skill points or by buying and selling in shops), and it is that skill that affects the items available for sale?
Romancing SaGa: Minstrel Song has shop levels; as you buy items (I don't remember if this happens when you sell), the three categories of shop levels will improve, and as they improve, shops will offer more items. (This game is open world, which is not typical of a JRPG.)
Disgaea has a shop level, which affects the most powerful items that the game's only store will sell you. However, to actually get the stronger items to show up, you need to go to the Dark Assembly and have them pass a (fortunately easy) bill; there's also a bill that does the reverse. (This game, a SRPG, has a base area from which you embark on combat missions; it is in the base area where you have the shop and the Dark Assembly, as well as a hospital that gives prizes.)
