I have no idea what really goes in within Square enix' walls outside of the heavily storied FFXIV disaster but based on that (as well as that wonderful FF7 post portem at polygon) , interviews with dev teams and trailers /etc over the last 10 years I can perhaps accurately speculate on why Square is such a disaster since the PS3 launched.
2001 - This was the year of "The Spirits Within" , a bigtime film investment largely spearheaded by Hironobu Sakaguchi coming off the glow offered thanks to a string of huge successes - FF7 and FF8. Square spent 3 times as much money building their movie studio in Hawaii as it cost to make any of their games and then they spent even more money making TSW which as we all know tanked hard at the box office. It didn't bankrupt them but all the profits they made off their entire PS1 library were gone. As well, FFX suffers a months long delay in Japan which also hampers it's US release where it is snuck out just a week prior to Christmas.
2002 - Sakaguchi takes the blame for TSW (and steps down from the company)and the movie studio is pretty much shuttered and sold off. So the company is without a proper pilot after many years of success and the downfall begins. With little cash on hand to expand Square merges with Enix.
2003-2004 - FFXI ends up becoming very profitable , FFX-2 is a success , Dragon Quest 8 makes it out the door and Kingdom hearts is proving a successful new brand. FFXII is announced and delayed. KH2 is announced and delayed.
2005 - PS3 alpha devkits show up and like many japanese developers , early tech tests push well past what the real hardware can actually do. Infamous FF7 demo shown at E3 inspires the FFXIII team to push forward with the new hardware , targeting what I can only guess is a 2007 release date. Dragon Quest 8 attempts to relaunch the brand internationally, it fails to meet sales expectations. FF12 is further delayed and it's lead director quits after suffering a nervous breakdown (probably from overwork). Kingdom hearts 2 finally launches about a year behind schedule.
2006-2009 - FFXIII engine is proving to be too ambitious for the actual PS3 hardware by a substantial factor , lack of proper direction and guidance from above is leading to a very slow pipeline of unusable assets being created for both it and the now well into development FFXIV. FFXII finally releases and a few months later also gets an international release... possibly 18 months behind schedule. Versus XIII is also revealed to the world. Despite all this , FFXIII does just barely creep out in Japan at the end of 2009. In an attempt to keep up with the demands of the gaming public , Square purchases Eidos in order to have an established western development arm attempt to keep them afloat in light of all the problems in their traditional asian business side.
2010 - FFXIII comes out in March , is revealed to be a shiny 30 hour long corridor with a half baked cast of marketable characters and a overly lore heavy backstory. It manages to sell well in spite of this. FFXIV launches to disastrous results just a few months later, adjusting the entire companies direction substantially going forward.
2011-2013 - Restructuring years at square enix , you didn't really hear about it but think back on just how many games came out during this period that were basically outsourced , direct sequels, remasters , etc. Nothing major outside of A realm reborn came out during this entire period. Versus XIII is shitcanned because the god awful engine powering FFXIII can't handle it at higher than 10 fps and the game design is a mess having spent so long in the oven that it's a bloated boring trilogy of Zippers and belts that probably wouldn't sell well (in light of the massively depreciated sales from XIII-2 and LR where they got beaten by a low budget 3DS FF Homage in sales). PS4 devkits arrive and it's decided that enough of the Versus XIII disaster is salvageable that they can release the game in 2014 on the console. Also infamously during this period, the biggest most expensive Eidos title - Tomb Raider , see's release and sells a whopping 4 million copies in a couple months but it's seen as a sales disaster because Square needed the game to prop up 3 years worth of under-preforming titles to keep shareholders happy. A Realm reborn also launches and it's really good ! in a continued effort to please their fanbase and give them what they actually want, Kingdom hearts 3 is also greenlit. The announcement to everyone coincides with the very early start of the games development. What we all saw at E3 for both Versus XIII/XV as well as KH3 were not real games at all. Just the same internal trailers required to get shareholder approval.
2014 - a few months of development in and it's proving that getting Luminous up and running on a PS4 will take at least 4 times as long as intended and the 2014 release date for FFXV becomes a pipe dream so the game is promptly delayed to 2015. Problems with the engine then cascade down to KH3 and it's development is switched the Unreal 4.0 with the hope being that it can be finished by 2016 with a more complete engine. Internally, Cyber Connect 2 has been commissioned to build a prototype/proof of concept for a FF7 remake project.
2015 - Episode Duscae is released after it becomes apparent that Luminous still won't be completed fast enough to even hit that entire year for release. As well, with all the money on the line , it's creation is deemed required to make sure the core game of FFXV is actually good. Luminous is finally finished later this year. So a 12 month crunch is initiated to complete FFXV for release In September of 2016. This is the only window of actual full development the game ever gets. In the meantime , KH3 is running massively behind schedule because switching the Unreal 4.0 wasn't the easy route to victory that was expected. FFXV's delay and A realm reborns continued success buy them some time though and a new release of 2017 was probably in the plans at that point. In order to spur more fans into upgrading to PS4's , FF7R is announced this year and even shown off. These are all lies though as CC2 was only ever brought in to build a prototype of the bombing run to demonstrate some concepts and determine how long it would take to build assets. Dragon quest XI is announced , intended for release on 3DS/PS4 in time for the series 30th anniversary.
2016 - FFXV finally makes its way out the door , half baked and buggy but otherwise a fun game with a terrible story. It meets sales expectations. Dragon Quest XI is delayed a few months. Work is completed on Cyber Connect 2s FF7R concept and by April , it's decided to end their working relationship and take the game internally but all 3 main teams are busy - FFXIV, KH3 and FFXV. An expansion is approved for 2017 to build FF7R properly in house.
2017 - KH3 by this point has undoubtedly received the same ultimatum from above that Tabata got in 2016 - "this game MUST release in 2018 no matter it's completion state". FFXV gets closer to being an actual finished game with each patch and update throughout the year. Final supplemental material is approved to be patched in through 2018 to make the game as finished as possible for work stops. Dragon Quest XI launches in Japan with a western release planned for 2018. From the start of April 1st through to march 31st 2018 a hiring frenzy begins to staff up a brand new team helmed by squares mobile division specifically to complete FF7R. Internally the first episode of this project is being aimed at a 2019 release to still launch on the current hardware generation. Based on everything I've just listed a delay to that goal in inevitable.
2018 to 2021 - Kingdom hearts 3 will finally launch , DQXI will come out world wide , FF7Repisode 1 will make it out the door and we'll see an announcement of FFXVI , it will aim for a 2020 release but probably get delayed to 2022. Eidos' Marvel games will make it out the door and probably fail to meet sales goals. In other words the square enix clock will keep ticking. The only constant is that FFXIV ARR will remain highly profitable and keep the company in the black.
I mean, this company has burned it's bridges , rebuilt them with better materials and then burned them again so I have little faith in them to deliver a big game on time with high quality ever again.