Plotholes are okay as long as you enjoy the overall experience.
HR fullfilled it's goal, as opposed to Fahrenheit, which went belly-up towards the end.
But Dave Cage said he's now done with this formula, the next two games will be "very different".
I'm still hoping for an adventure-RPG Omikron 2 with a huge breathing world and super-duper silly characters. I'd buy it.