The 3rd season wasn't nearly as bad as some have made out. To me it easily - EASILY - beats out some of the other spin of series, let alone the vast majority of whats on TV today.
That all aside, my "improvements" may be akin to splitting hairs:
- have Shatner return to his shorter, better kept season one haircut
- that they never would have made Plato's Stepchildren
- that the money saved from not having made Plato's Stepchildren could have been used to create a few key, truly Romulan ship interior sets for The Enterprise Incident
- that they would have replaced The Mark of Gideon with a follow-up to The Enterprise Incident, this time reusing those newly made Romulan ship interior sets and giving us something more interesting AND plausible
- keep Scotty fully in character for The Lights of Zetar, yet tweak the story so that it has both depth and character development
- have a more realistic and better time lead-in to McCoy's health resolution on For the World is Hollow....and maybe make his separation from his new wife (a Rocket Lady) a little more realistic
- find a way to keep Eddie Paskey on the show, maybe kill him off in Wink of an Eye instead of/or as Compton, and bring him back again a week or two later.