Sounds like it was in development, ran into performance issues, was put on hold, with new Japan Studio management was started up again with additional help but put on hold as the hardware wasn't powerful enough. Then came the bit where Ueda left and set up a new studio, PS4 development spec was probably shared and Ueda brought back in and the project resumed under a joint team.
Ueda probably wanted to release the game with an install base of 80k and wasn't happy until two things happened:
1) better hardware and easier to work with
2) the PS4 getting the reception it did
I think Ueda aimed really high and got burnt out in the process of being unable to bring his vision to life. As he says, he is more of an animator than game developer and the new set up, although he was unsure of it first has worked to his advantage. He can basically animate and create stories whilst Japan Studio do the heavy programming, engine building etc.