The most common complaint from the producers seems to have been too much dialog, not enough actual plot or involvement from the heroes. I can think of a lot of fan film episodes that suffer from the exact same issues.
The staff loved to complain about stories that came in where Kirk did not drive the action...and where there wasn't enough action, period. I shudder to think what they would have written about the scripts that have actually been shot for most fan films — even the ones with adequate production values usually have the same issues.