I do prefer the First Five year mission ending with Where No Man, The Second Five year mission starting with The Corbomite Man and ending with Counter Clock, The Third Five year mission starting and ending with the comics and novels, The Fourth Five year mission starting with TMP and ending with the comics and novels.
I am using what is in the show and the movies.
It's true, any story set during the Fourth five year mission is usually better in the comics than the novels. I'm trying to remember any of the novels that are good. . . Off the top of my head, 'Time for Yesterday' and 'The Romulan Way'.
Then there is the Kobyashi Alternative game set during the fourth five year mission and the Starfleet Academy set during the fifth.
I don't like would happened in TFF and TUC. Most of them should have been transfered to the Excelsior. Shake things up.