I think Gene would have revise that for each series (and each series of movies).
True. According to Paula Block, he considered The Original Series to be apocraphyl once Next Gen began.
"Another thing that makes canon a little confusing. Gene R. himself had a habit of decanonizing things. He didn't like the way the animated series turned out, so he proclaimed that it was NOT CANON. He also didn't like a lot of the movies.So he didn't much consider them canon either. And--okay, I'm really going to scare you with this one--after he got TNG going, he...well...he sort of decided that some of the Original Series wasn't canon either. I had a discussion with him once, where I cited a couple things that were very clearly canon in the Original Series, and he told me he didn't think that way anymore, and that he now thought of TNG as canon wherever there was conflict between the two. He admitted it was revisionist thinking, but so be it."
That's why I don't take "what Gene would have wanted" seriously. TNG as the ultimate incarnation of Trek... *shudders*