My gut instinct is by the time Ellison delivered his first draft script their conception of the show and its characters had solidified from where they were when he pitched the thing, and then they flailed in figuring out how to fix it, by which point I suspect Ellison got his dander up. The memos I've seen and the various drafts by the staff indicate to me that no one seemed to "get" the fundamentals of the story and thus they were missing some really obvious structural fixes they might have suggested to Ellison. Of course, all we have access to are the extant memos and documents that still exist and are available and are not privy to what was discussed in person or on the phone. Steve Carabatsos' Oct. 1966 staff rewrite attempt illustrates this in spades, as he "fixes" things by breaking others (i.e. introducing Trooper as soon as they arrive in the past and then forgetting about him, as opposed to Ellison's draft which brings him in out of nowhere in the last act without any setup).