Here's why:
1. Ward limits on retainers.
This is the biggest issue with Market Wards, and it's happening NOW when the servers are at extremely low populations. This problem is going to get more and more noticeable as the game increases in popularity (if ever). Most solutions to this introduce a whole bunch of other problems, so let's go over those.
"Increase the ward size!" This places an increased load on both the server and the client. Servers must store information of what the retainers are selling/buying/reparing, what they're holding, their locations, and their texture meshes (and probably a bunch more that I'm forgetting). The client has to wait until all of the retainers load and are painted over with textures before being able to access them. In addition, large market wards become extremely tedious to search through, even with a search function, because you still have to run your character through.
"Break up the wards by level!" One of the better solutions, but this makes it an inconvenience for people buying items at different levels and a HUGE inconvenience for people selling items at different levels.
"Duplicate wards!" Overall the best solution, but it still has the same problems as the two above. Increased server load, zoning between wards, tedious to search through, etc.
2. Penalty for selling in the wrong ward
This is also a very anti-seller problem with Market Wards. Anyone trying to sell multiple categories of items will be forced to take a tax penalty on items in the wrong category. This might not seem like a huge deal, but it is a pretty big turnoff for gathering classes, who don't just get one kind of item.
Keeping track of multiple retainers if you want to be able to sell without penalty is not feasible, especially since extra retainers will cost money and will be unavailable to transfer items to and from for storage purposes. Removing the penalty for selling in the wrong ward is pretty much like going back to how wards were before they were broken down by category, so that's a no-go as well.
3. Forced zoning
This is something that is impossible to get fixed while still keeping Market Wards as Market Wards. Huge inconvenience.
4. Limited sale slots
There are way, way too many synth materials and items in this game to realistically fit all of those on one retainer and try to sell them. There's NQ, +1, +2, and +3 qualities of practically every item, and I almost permanently have inventory issues as a gatherer. When it comes time to offload items to sell on my retainer, this becomes an absolute nightmare, because I can only put up 10 items for sale at a time.
This is big. Limiting the amount of items people can sell is going to ensure that A) there's going to be price wars and undercutting, because the time in which an item sells is more important than the price for which it sells; and B) more unpopular or low profit crafting materials will likely never be found on the AH.
5. Crash issues
An Auction House is made with a simple MySQL or Oracle DB. It is inherently crash resistant, because even if it goes down, the entries in the DB will remain in the DB until removed.
Market Wards, on the other hand, are not crash resistant. When the MW service goes down, retainers are reset.
I'm not going to speculate on whether it's possible to make retainers not reset during MW outage, but I am going to say that making an Auction House is probably way, way easier than finding the workaround for retainers.
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My Solution
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Don't remove the Market Wards. Improve them as best as you can. They can still function like the bazaars that many MMOs have.
But an Auction House needs to be implemented. The overwhelming majority of MMO players today expect an intuitive, AH-like system where you can get all of your item trading done from a single window/NPC, fast, with extreme ease, and no inconveniences. AH systems are pretty much standard in MMOs, and have been since FFXI.
In addition to Auction House, we need to review the rate at which items enter and leave the market. Western MMOs like WOW, Aion and RIFT have mechanics by which you can destroy unwanted items to gain useful materials. This is a vital aspect of their economies, but this is another topic for another time.
Bottom line: AH is an easy to implement solution that fixes practically every problem with Market Wards.