*Gasp* People need to play the game for rewards? Heaven forbid they do that.
Your comparison to the market boards is also flawed as gil in the game is (For the most part) Only achievable by again...playing the game. Rewarding the players for...playing, this allows them to focus their efforts in fields they enjoy and use Gil to bypass some systems such as farming or gathering, where as those that supply the stock for the markets benefit in kind by providing others with a service they wish to not do themselves.
All of this happens in the game with no influence from the outside world other than the players interaction with the game and community, and these actions benifit all players by keeping people in the game and playing with eachother. purchasing something from the mog shop does nothing for the community nor does it involve the game in any way other than your interactions with your rewards after purchase. It's just bad game design to encourage people to NOT PLAY your game, sure the financial gain in the short term is good (Perhaps even great) But it damages your long term prospects.
Removing potential content, rewards, incentives, goals...all of these act to detract from the overall game experience for your players. Many may consider it a "Convenience" in a way it is, but it is also actively encouraging you to not play the game itself and instead designed to quickly spend your vested interests in short term cash purchases instead of investing the resources into the game itself.
It's not hard to wrap your head around business wise it's a good idea to extract as much cash from a property as fast as possible, they never know when the next WoW will release so why bet on the long game of retaining subscribers when they can get the cash now and players are more than willing to oblige?
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More to your original point. Why not both sides then?
Why not include the content in the game behind content and purchasable in the cash shop... Would not that actually be the most consumer focused way to introduce some of this vanity content?
I mean who would it hurt if that moogle mount could be earned through finishing the moogle beastmen tribe that takes weeks of dedicated playtime to accomplish...or to purchase it with cash to skip the actual work? As long as they kept the majority of the games content as...content only rewards I would be OK with the general cash shop content existing in both realms attainable ingame and out of game.