I don't know that that was a result of Star Trek filmmakers emulating other Star Trek filmmakers.I think most later Trek movie makers came away with the wrong lessons from TMP's failings and TWoK's successes (with a long line of petty, relatively dull villains like Nero, Ru'afro, Soran, Kruge, Khan 2.0, and Shinzon, etc).
For one thing, TVH was quite successful, and a departure from the villain formula. If what you say were going on, then I'd think that TVH would also have been a prototype for future films.
For another, the assumption that every protagonist needs an antagonist comes from the general theory of narratives™. It's not confined to Star Trek.
