I like the idea of a Muslim chaplain, and that is the correct term by the way. A religious leader in Islam can be called an Imam, but in a military sense, ‘chaplain’ no longer refers to just Christian clergymen. Muslimchaplains.org’s very existence attests to this. Making Uhura a Muslim is also a neat idea, as is expanding the character’s role from “woman with thing stuck in ear”. I wouldn’t conflate and confuse things my making Uhura the chaplain, though. That role should be filled by a separate character. It could be interesting if they were from different factions of Islam, or at least had differing viewpoints & didn’t always get along.

Mudd was a great character in both of his episodes. I would try to avoid him being used just as a comedic foil. I would make him more like Baltar in the original Battlestar Galactica, if more money-hungry than sinister. In a nod to the character’s last appearance on TOS, I would have him on the run from both an estranged wife and super-advanced androids. Though I am normally all in favour of characters that are not top models–dumpy & homely, even–I would make Mrs. Mudd smoking hot. The audience should (at least at first) be perplexed as to why the same guy who is calm & cool about keeping away from the super-intelligent & super-competent androids (who can also perfectly create a mimic of any person) is frantic and panicky about the idea of even being on the same planet as his wife. In a later episode, I would try to turn the audience’s confusion into genuine sympathy for poor old Harry by her doing something so horrible that no one could help but feel sorry for him.

For the new Kirk I would not have him start out as Captain. He would be the First Officer of Cpt Pike. Kirk loves the privileges of rank, but without the responsibilities of actually being in command. One thing that has been keeping him out of the big chair is his inability to keep Little Tiberius in his pants. Pike dies in the pilot episode, and Kirk has to take charge. He still has trouble delegating, and may even have a death wish, which is why he leads away-teams himself.

I would also show more of civilian life than other Trek shows have. Part of Roddenberry’s original idea was that this was a near-idyllic society, what humanity could grow up to be if it got over some of its current deep personal issues. And bad acne. My father had a theory that the officers of Starfleet were the handful of people in the UFP that have too much drive and energy. Most everyone else stays at home & watches television all day. By making Jody-on-the-block a lazy, whiny, worthless sponge of a human being (or alien), then it makes the Enterprise’s collection of violent and reprehensible misanthropes seem more heroic in contrast.

I really like the transhuman colonies idea. This could be used to great effect to explore just what it is that makes us human.

George Takei as Q
Wil Wheaton as the Squire of Gothos

Cameos from actors from other sci fi shows. Good guys as bad guys, and vice versa.