Kojima did not waste money, he developed an entire engine that they are still currently using for PES, along side helping produce some non MGS games for Konami, and pushed out peace walker as well. He also sat on the board of directors for konami.
Fox Engine started in ~2010, after peace walker, We heard about "project ogre" in 2012. We got MGSV in 2015, and it came on 5 different platforms and ran well on all of them. Most AAA games coming out today take about that long and run iffy.
In contrast
GeoW 4 took 5 years
UC 4 took 5 years
GoW is still not out
Crackdown 3 is still not out
Horizon will be an estimated 6 years when its released (began in 2011).
You get the picture. Non annualized games, AAA games take time. And those are ALL exclusive.
The main problem was, Konami changed presidents, and then, changed directions as a consequence of that. Focusing more on mobile game development and yearly franchises (PES). Obviously MGS has NEVER been a yearly franchise so there was going to be a problem.