Sticking my nose in here, but on the story front, I really don't think all the professional episodes always stand up either. It's only because they define cannon that people find a way to make them consistent with it. Plenty of the pro stories are internally inconsistent also.
I find many of the fan films may have less smooth writing and technical standards, but for me, the love goes a long way. Some have serious problems with the acting, though. I admit that part of the joy of viewing (and I speak only as an avid viewer, I can't imagine the circumstances that would lead me to make a fan film) is the intimate feeling you get watching it. It gives it a campfire story quality no pro show can match.