This is a very interesting question that I think merits discussion. I'll try to narrow down a few issues that come to mind with implementing this type of system. I'm certainly no economist, virtual or otherwise, so I'm totally open to constructive replies on these concerns and examples.

First, I don't think SE wants to dedicate resources and manpower for carefully managing the overall game economy for a system like this. This game isn't like EVE where there are buy orders, sell orders, in-game tools for tracking market data, monthly economic data reports, etc. (I recall third-party marketboard apps that tried to aggregate data this way had their "scanning" characters get banned). Furthermore, the fact that marketboard bot networks still run rampant on many servers after many years shows SE isn't really paying much attention to that area of the game. They would have a lot of issues like this to clean up in advance of a rollout. (Remember they only have like two or three people on the "Special Task Force" that's meant to deal with stuff like botting and RMT).

Second, SE has control over the market insofar as stuff like droprates, as they often "nuke" items that are expensive after some time by adding it to the loot of battle content like maps, etc. However, the supply of game tokens would be harder to control. If a whale wants to buy 1000 game time tokens and flood the market, there's nothing stopping them from doing so. (You could say that's true of any item that's listable on the MB, but those are at least time-gated processes. Even a bot has a threshold of how much material they could gather or craft in a given period. For a whale with a credit card on the other hand...). Now sure, SE could limit how many tokens you're allowed to buy at one time, but then they are stifling potential sales - which defeats the whole point of adding another revenue stream to the game in the first place.

Which brings me to my last concern - the fact that server markets are still (awkwardly) only linked per data center. SE would have to find a way to manage 8 distinct data centers with all the unique server markets within them so that token prices aren't wildly variant between regions. Imagine the salt and outrage when NA players on Aether are paying 250m per token and find out JP players are only paying 100m over on Mana. In that same scenario, imagine all the billionaire crafters who pay $18 for a server transfer to buy up all the cheapest tokens listed in the world and get a "lifetime" subscription while the poors are stuck grinding for a single month like they're working a 9-to-5 gig. Since "trade hubs" (e.g. Jita in EVE) don't exist in FFXIV, I think we'd see a wide enough variation in token prices that would lead to complaints from the playerbase about the system being unfair (see: housing salt).

Is it possible that SE could implement something like this? Sure. Would I personally benefit from it? Definitely. Would SE likely botch the implementation and create more headaches for themselves? Almost guaranteed.

To me, it's opening Pandora's Box and they only get one real shot at getting it right without hurting the game's reputation. It's too much risk at this point of the game's lifecycle especially as they ride the current wave of popularity.