People who worked with Roddenberry remember that he used to handle
canon not on a series-by-series basis nor an episode-by-episode basis,
but point by point. If he changed his mind on something, or if a fact
in one episode contradicted what he considered to be a more important
fact in another episode, he had no problem declaring that specific
point non-canon.
See, people can easily catch us, and say "well, wait a minute, in
'Balance of Terror', they knew that the Romulans had a cloaking
device, and then in 'The Enterprise Incident', they don't know
anything about cloaking devices, but they're gonna steal this one
because it's obviously just been developed, so how the hell do you
explain that?" We can't. There are some things we just can't explain,
especially when it comes from the third season. So, yes, third season
is canon up to the point of contradiction, or where it's just so
bad... you know, we kind of cringe when people ask us, "well, what
happened in 'Plato's Stepchildren', and 'And the Children Shall Lead',
and 'Spock's Brain', and so on — it's like, please, he wasn't even
producing it at that point. But, generally, [canon is] the original
series, not really the animated, the first movie to a certain extent,
the rest of the films in certain aspects but not in all... I know that
it's very difficult to understand. It literally is point by point. I
sometimes do not know how he's going to answer a question when I go
into his office, I really do not always know, and — and I know it
better probably than anybody, what it is that Gene likes and doesn't
like.[3]— Richard Arnold, 1991
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.[4]— Paula Block, 2005