I'm told that, besides general competence issues and political-football games about who gets to builds the subway (contractors, ewwwwww) ... a lot of it comes from deep stations with onerous fire-safety guidelines that require massive mezzanines. These stations are mined out through narrow shafts instead of doing cut-and-cover, adding expense and inviting delays. See e.g. https://twitter.com/2AvSagas/status/1064907564230557696

But it's mostly the fact that the leadership doesn't care, doesn't have to care, and is actively incentivized not to care.