I know where it all went wrong. The cover. Prototype's tape cover shows a fake-looking robot standing against the background of a virtual reality grid. Instead it should have been showing a couple of lovers with expressions of suffering on their faces and some kind of dramatic quote. The movie should not have been called "Prototype" but rather something like "Desert Roses". It would have attracted a different kind of audience and would have perhaps been much better received.
Even if the people watching this B-movie do not admit to having any expectations for it, they are subconsciously expecting to see indications of some genre. Yet they receive none because Prototype can't pick a genre. Well then, is it like one of those smart genre-transcending films? Well, no. Firstly, because it is not smart and secondly, because even those kind of movies are clearly about something and generally pick an emotional focal point out of each genre on which to base the storyline and Prototype doesn't really get its footing in any of the genres. However if we tried to pinpoint a genre, it would most definitely not be an action movie, but a drama. It is a poorly executed drama.
The story is about a problematic couple getting caught up in the leftovers of a vague futuristic conspiracy. The setting is an 80s post-apocalyptic world.
There are multiple aspects of the story that could have been much better developed. It is not that the movie does not have enough material, like some have suggested. It is that the makers did not do enough with the material at hand. There is a whole movie out there about nothing more than a guy who gets his hand stuck in a rock, and it managed to keep its audience interested. Prototype is just poorly executed. The few action scenes are laughable. The stuff in between the action scenes doesn't have enough expression, contains horrible camera decisions and is in desperate need of better dialogue.
Having said that, the movie is somewhat underrated as it does have an interesting style and the acting, which this movie heavily relies upon, is not that bad. Unfortunately its style is a slow one, and unless you have a lot of patience with pessimistic sci-fi dramas, you will not like this.
I wish someone redid this movie and gave it life rather than a zombie existence.