I think it has more to do with SE's relationship with fans for the last 10+ years. We went from watching Squaresoft push out tons of great FF titles accompanied with other great franchises like Mana, Front Mission, and Chrono to suddenly have Square0Enix, which releases an actual numbered years after being in development hell, making sequels nobody asked for and some other fans question the logic of doing.

I mean FFXIII sold really well but received a lot of negative feedback from players, then SE turned around and made a sequel for it which only a part of the fanbase actually cared about and that game sold only half as well, and now they've announced a third game despite saying they were not going to do that. FFXIV was a disaster that made SE's president actually apologize to fans, and we can only wait to see if XIV 2.0 will do well or if the damage from the initial launch may have hurt the games rep, especially since we're now going into an era where MMO models are changing and free to play games are gaining more ground, but that's a discussion for another day.

Versus XIII itself is trapped in development hell, to the point the company is forced to make statements just to confirm it isn't vaporware.

KH is a huge success for the company, but six years without a KH3 and releasing four titles spread across three different platforms has alienated parts of the fanbase and may have set itself up for disappointment when KH3 finally does arrive and 3/4th of the fanbase get annoyed cause they have to play the game with the KH Wiki next to them just so they can understand what's going on.

Cries for a VII remake are ignored despite it being the number one thing fans have been asking for years.

While their in-house has had some modest successes, they just are not pulling out the type of content that becomes household names anymore. I mean their biggest titles in the last years are from the Eidos branch they bought as the OP mentioned. The company is making more bank as a publisher in the West than as a developer. Sure they are making money, but they've really wrecked their franchise's reputations.