Some very good points being made but there is a prevalent point of view I'd like to address
Pehapes I'm too dense, but quite frankly I don't understand how your analogy relates to the point that I made, which in case if you forgot, is to allow seller the option to choose whether to sell a stack as bulk or individual items.
The first point you made that "people will only buy items from the lowest price/item in the market." is irrelevant because even if sellers are allow to sell each items in a stack individually, the ones being sold in bulk will still have a discount because seller will set different prices just as they would when you have to put each item up one by one.
I believe yours and many others' issue is with HOW MANY single item a seller is allowed to put on the market, which is what giving seller the check box without adding additional limitation would result in changing. While a person selling 40 individual items will have to use up 40 retainer slots to put his inventory on the market with the current system, he will only have to use 1 slot to put those same 40 items on the market if you give him the ability to sell a stack as individual items.
Also, I'd like to point out that just like Elasia described, the current system does nothing to stop RMT from making a tons of alt and undercutting others by making a million mules to get the job done. In fact, I'd think the situation would be worse because a player would have to scroll through 8 pages of cheaply farmed material that an RMT can put up on the market board with a script or bot program, while legitimate player would have to do the whole process by hand.
However, I believe that same limit the current system enforces can easily be achieved WITHOUT making the UI clunky and horrbily inefficient to use. Under the current system, the seller will have to click on an item, set the price and the size of the stack one by one until he does the whole process 40 times just to put his inventory on the market and the buyer will also have to click on 40 individual items and buy them one at a time if he wants 40 and not 99 items. On the other hand, if you give seller the check box to sell a stack as individual items, you can STILL make each item he has in that stack take up one retainer slot while selling a whole stack in bulk will also take up one retainer slot, this way, the artificial limit SE places on the seller will remain unchanged, but the usability of the market board will be significantly improved.
To make my very own analogy. Angry Retailer, my Roegadyn retainer, owns a stall on Saphire Avenue Exchange that has 40 shelve spaces. He has an inventory of 99 fairy apples to sell. However, Yoshida, the almighty god of Eorzea, has decreed that you may only put ONE apple on each shelve space if you'd like to sell them individually, further more, you are only allowed to carry out one apple at a time from the storeroom two blocks away and must also label each one individually; alternatively you may magically shrink a sealed barrel of 99 apples to fit on one shelve space instead. Because this is such a pain in the ass to do, Angry Retailer decided to ask his fellow merchant to rise up together to protest this decision. What they propose instead is to either sell the magically shrunken barrel of 99 apples taking up only one shelve space, or to sell a normal unsealed box of apples that would take up as many shelve spaces as there are apples in the box. And this, my fellow merchant, is what I believe can be done to maintain the same limit of how many individual items a player can sell at a time without sacrificing usability and making everyone's life miserable.