It's hard to really know what rating to give pathogen. On its own, it's pretty flawed. Indeed, the commentary almost plays out like a riff track with the actors pointing out the many problems with continuity, extras, props, etc. But the reason for this is the same reason I'm giving it such a high rating. It was made by kids. And not kid in the sense of Matt and Trey when they made cannibal the musical in college, but kids in the sense of just getting into junior high.
Watching it is almost like watching someone learn to speak, or paint, or draw. Or anything which is going to eventually become second nature, and which has a strong tradition the person is unaware of. But for those first steps, the first paintings, they're unaware of it or only know about it in the pererpheral sense. In a real way those first tries are inventing the thing for the first time.
And that's what we see in pathogen. Actors in their first roles, with one notable exception. Writers and directors who are only just figuring out what works and doesn't. But learning from the experience. In the process of start to finish you can see an amazing growth in everyone involved.
Which is the other great thing about this movie - the love. The people in this movie obviously love being in it, and it's hard to not catch that feeling yourself while watching. It's totally clear that everyone is having a great time with it, and loving everything about the process. From the actor doing a little dance in the pizza line, to the hallways with a smattering of students all walking the same direction. They're all just obviously having a great time, and loving the process.
The movie itself, on its own, is actually pretty good as well. Raw, obviously. Odd for some of the problems in filming, sure. But it works. I had fun watching it, wanted to know how it would turn out, and wanted to shake my first at the character when a reveal near the end came up.
Also, watch the movie with commentary. You really don't get the full experience until you'e actually heard the experience of everyone involved. The cast watching the movie and talking about it really is as much a part of the movie as the actual plot itself.