I think it's a fair criticism that fan film scripts can fall short from not having that one hard-boiled set of eyes looking for ways to push, pull or cajole writers into improving their scripts or failing that to do a necessary re-write. It's fascinating when you look at the background of the TOS classic episode "City on the Edge of Forever". It was rewritten so many times that nobody knows for sure who deserves credit (or blame) for certain changes. However it's always at or near the top of the list of nearly everyone's "best of" lists. Contrast that with the third season where GR, Dororty Fontana, Gene Coon, et.al were gone and look how many weak stories there were compared to the first two seasons. I'm not going to say that "And the Children Shall Lead, The Way to Eden or even Spock's Brain could have beenn turned into classics, but I do think that when you connect the dots and look at the writing process for season 3 and who was overseeing it, and compare it to the first 2 seasons it's pretty easy to conclude that writing and script supervision simply wasn't up to snuff. (no knock on Fred Freiberger, who turned out some episodes that were as good as any in the first two seasons, but just didn't have the support structure IMHO that would have raised the floor on some of the clunkers.)
ETA: I think that Phase II suffers just a bit from hero worship with these excellent writers. I felt that Blood and Fire came across as too much of a polemic and that it would have benefited enormously from one or two more re-writes. Again, that's no criticism of Phase II. What they accomplish is nothing short of amazing and any criticism has to be kept in perspective.