Yeah, all the body parts floating around was kind of lame. When I rewatched this on DVD, I turned on David Gerrold's commentary, he had a few interesting comments about it originally being submitted for the live-action show. His original idea was for a strong short actor carrying another lighter short actor on top of his shoulders and that they would be costumed as a 2-part alien. The top part would jump down off the bottom part and walk around as separate beings. Why this couldn't have been shown in the final animated form instead of all this floating stuff is the big question.
He introduced the idea of Spock having a logical reason for being prejudiced against Bem since Bem was a "practical joker" but I never saw much of this idea surviving to the final script. Perhaps it was just as well.
He also claimed that it was Gene Roddenberry that wanted the crew to find "god" on the planet. So he had to write that part into the script that Nichelle ended up doing the voice for.
I may be wrong but I seem to remember that giant clones and talking plants weren't part of Walter Koenig's original script for "The Infinite Vulcan" either.