Ultimately its downfall was that the mental patients were left to run the sanatorium. There were too many big ideas, and themes that were going on at the same time. The creators had a grandiose idea, and were not able to properly execute all of their ideas. This anime is a classic case of "less is more".
It is a shame too, because Robotics;Notes was a promising anime. The characters were not bad by any means, and the setting was done well, and the animation and soundtrack were top notch. Where this anime REALLY shines is the set up. Robotics;Notes creates this incredibly eerie set up to the events which take place. It send is an intense atmosphere that almost sends shivers up your spine. Unfortunately what comes after is either not so good, or makes no sense from a logical standpoint.
My last thought on this anime is I felt as if they were trying to create another Steins;Gate. The premise is different, but many of the events, conspiracies, and such all seem like they were a cheap rip off of Steins;Gate. They were trying to replicate the formula which brought them success, but failed.
This is a good anime to watch if you have nothing else to do, and are looking for nothing but a time waster. This anime was mildly entertaining, yet disappointing. If you can accept the fact that it is not Steins;Gate you may find yourself enjoying it.
