Script revision is one of the "under the hood" issues for fan films that is always going to be difficult to solve. Coming up with a coherent story and turning it into a viable (for the medium) script are both extremely difficult. But "coherent" is not the same thing as "professional quality". I really think that the most important part of GR's role as showrunner for TOS (along with Gene Coon and DC Fontana) was in making sure there was an overall continuity to the way the characters behaved. I think the most valid complaint about this script (which I think is quite good in many ways) is that the constant references by Kirk to "consensus" does go "clunk" for those used to Kirk's ability to make decisions and willingness to take the heat for them. Command style is one thing that should be no matter who writes the story. I don't know if there's ever going to be any way to really solve that issue with a fan production, where someone can point out the flaws, false notes and inconsistencies for one last re-write that takes a show from the realm of serviceable entertainment (which I think is a remarkable achievement) into a high level.
The first two conference room scenes were completely consistent with TOS and how Kirk would sometimes bring in staff to discuss an issue. A simple rewrite eliminating the final conference room scene and incorporating some of the dialog into the sick bay scene following Apollo's sacrifice would have tightened the story and made it more in line with how TOS flowed storywise.
But honestly it's a pretty small nit, and I feel "Pilgrim of Eternity" is the one fan film which really captures the story structure and morality play feel of TOS better than most others. Heck my only real beef was the final scene of the story ONLY because TOS probably would not have shown Apollo committing an act of kindness and would have instead left it up in the air as to his fate.