I think they could have made it work if they had laid their cards bare in the middle and not attempted to surprise the player with the plot.
They are chiefly up against the Matrix with an architect type character at the end responsible for the workings of the system , and in a wider sense both popular and less known Sci Fi culture and canno, all of which has already been analysed and discussed at length.
Being an 'RPG' they are in my mind also up against the ending of DX1 and DXHR, an AI at the center of the discussion and a prominent 'father figure' of synthetic life (Bladerunner, I Robot, BSG, and many others). They should have acknowedged this legacy and written an intelligent take on the issues involved. It need not have entailed a dozen different endings, but it really needed good dialouge, not just a door '1, 2, or 3' solution. They could have had a strong card like Martin Sheen at the very end arguing out his position alongside the player for instance.