Basically FFXIV 1.0 failure and the development hell of 2.0 killed every single other projects after the PS2 gen.
SquareSoft also diversified it's offering by acquiring a lot of other companies, starting with Enix, but also less likened studios (ie: Crystal Dynamics).
After that they finally started to manage properly, which probably lessened their studios'"soul". They went from managing a few studios to being an gigantic editor after all.