I strongly suspect that Shatner expected Roddenberry to embrace his story about a search for God, because it had echoes of previous Roddenberry themes - but he ended up getting quite public anti-Sybok critiques from both Roddenberry and DC Fontana, who even quoted her old TOS studio memos regarding her attempts to keep Spock "without siblings" so the character would not be watered down. In her novel, "Vulcan's Glory", she deliberately had Amanda state that Spock was "the only son of Sarek". (I once told her in a Q&A that I suspected it was on purpose and she winked and agreed.)
ST II did have Lt Saavik, who was based on a young male Dr Savik from a different ST II pitch, and that Dr Savik may have had roots in Lt Xon of "Phase II", although it could also be coincidence.
Does anyone know anything more about that Samuel Peeples script? I've heard the name of it, but it eludes me.... other than that, I know absolutely nothing about it.