Yep. I've done a lot of
Star Trek rewriting in my head.
I'll limit myself to my Big Three Demands:
Borg - Cool it with them after
First Contact. Rescind the whole Borg Queen notion (it was probably necessary for the movie), and institute strict instuctions that nobody is ever allowed to be assimilated and then de-assimilated ever again; have the Borg permanently assimilate a main character (I would have done that rather than introduce Seven on VOY - have Paris or somebody become a recurring Borg character who is with the Collective, not on the ship); and not allow the Borg to lose fights with the Feds any more often than one time out of ten.
The Borg lost credibility the way they were kicked around and turned into jokes, and all they have is their credibility. Oh, and no Borg dissenters or any of that other crap. The Borg work best when kept very simple and straightforward. They should be used sparingly and when they appear, they should be more terrifying because of that.
Sisko - I'd put him on a different character arc as of "Rapture" (mid-S5). By telling the Bajorans to stay neutral in the war, on orders from the Prophets, Sisko sided with his role as a Bajoran religious figure over his duty as a Starfleet officer. He advised the Bajorans to go against Federation interests, on orders of alien beings who very well may have been in cahoots with the Dominion - or at least Starfleet would have to be very gullible, if not stupid, not to worry about that possibility.
Rather than have Starfleet be weirdly complacent about the commander of a key outpost in time of war doing something that could be interpreted as either moronic or treasonous, Starfleet should have pushed back, telling Sisko that he needs to choose Starfleet or the Bajorans. They can't afford divided loyalties. The shootin-war that breaks out not long after "Rapture" would have back burnered this story but it would have returned as of mid-S6 and should have been a central theme till the end of the series.
And there's no need to worry that the story would have been screwed up by having Sisko booted from command of DS9 - since that would have antagonized the Bajorans, Starfleet would not have been able to do that. But having hands tied by a bunch of religious fanatics and a rogue Stafleet officer should not have sat well with Starfleet - I wanted to see a lot more drama on that score.
Dukat - Making him a true believer of the paghwraith was silly. It would have been far more in character for him to cynically treat the paghwraith as just more aliens to be manipulated in his grand schemes of power. And very true to the character that he would assume he could "handle" them. Having Dukat be more in control of the situation and thinking how to turn it to his advantage, combined with Sisko who is losing the backing of Starfleet yet adamantly convinced he is on the right path, could have made the final showdown between them more than just silly video-game level nonsense. It would have been cynicism, represented by Dukat, vs faith, represented by Sisko.
