Well, although „to” can be translated as "is" in certain sentences, it isn't actually a verb. „To” means simply "it". So a sentence like „ryba to zwierzę” literally translates as "fish – it (is) animal”. It might sound primitive that way, but it's perfectly valid Polish sentence.
So when you see such sentences with „to” but without „jest”, the latter word is still assumed to be there. You can also include „jest” and that's too perfectly fine.
This also explains why you would negate sentences with „to” as „to nie” rather than „nie to”.
Ohhh, wow. So the lack of jest in other sentences is just some kind of idiomatic shortcut and they're in fact the exceptions to the rule? Why then do you not need to use the accusative for sentences of form "noun1 to noun2" but it is being used here? (Sorry, I'm not trying to argue that I'm right or anything - clearly I'm not. I'm just still a bit confused as to how this thing works.)
I don't know if comparing it to "Autumn IT is not..." is a good idea, because the English sentence does not look natural to me (if it's even correct...), while the Polish one is perfectly natural.
About "Jesień to nie dobry okres", I wouldn't recommend it. Why? "Jesień to dobry okres" is definitely fine... But when you add "nie", it kinda looks like a mistake in negating the adjective "dobry". "nie" is written together with adjectives, so the negation of "dobry" is "niedobry". I don't know if your sentence is wrong (if we assume it has an invisible "jest", it makes sense), but I would really recommend putting this "jest" explicitly and going with "Jesień to nie jest dobry okres".