Then why were they having such trouble securing the funds for ZE3?
Because Virtue's Last Reward sold less than 999 despite being on two platform and having a much higher budget (fully voiced, detailled 3d models, some 3d cutscenes, cost of developing on two different platforms...) than 999.
NDS Zero Escape: Nine Hours, Nine Persons, Nine Doors 16,967 / 44,367
3DS Zero Escape: Virtue's Last Reward 7,890 / 17,913
PSV Zero Escape: Virtue's Last Reward 6,133 / 15,454
They tried to expand the audience of the series by giving it bigger production values and it failed basically, sales would've probably been pretty similar had they stayed with a simple presentation like 999, and we would've gotten ZE3 years ago already.