Except for those parts of the canon, that are outdated, cumbersome, sexist or generally reprehensible or anything else that could get in the way of telling an interesting story.
I certainly agree that facts in the canon that are "sexist or generally reprehensible" should not be adhered to. That's really just basic morality. If the only possible way to interpret Turnabout Intruder is that Starfleet had a policy preventing women from being captains, I would not adhere to it unless I was telling an interesting story about how that policy came to be and how it was ended.
“Except” or “anything”?
The category of "anything else that could get in the way of telling an interesting story" is so broad as to be meaningless. As stated, it is really just a license for lazy world building. Which, of course, is self-defeating. It strains the suspension of disbelief beyond what is sustainable – the suspension only works if the rules of the fictional world are internally consistent. Furthermore, why bother telling a story in a setting that inspires the author if that author doesn’t follow the setting?
For example: Let's say I am fascinated by ancient Rome. I some interesting story ideas and I want to write a novel in the historical setting of ancient Rome. The canon I am working within, therefore, is what we know about ancient Rome.
You know what I also like? Laser swords.
I have an interesting idea about a story involving centurions who are armed with laser swords.
Also robots. The members of the Roman senate are robots.
My interesting story will still have the stone and marble of ancient Rome, political intrigue, the struggles of empire, and all that other Roman-y stuff. But also robots and laser swords.
Of course, I could tell such a story, IF I set it in the context of alternate history, a fictional setting.
But if my story is interesting, under your rule I am free to tell that story in ancient Rome, since adhering to the established facts would otherwise prevent me from telling it. Could I claim that it is consistent with the canon of the setting I have chosen (namely, historical, ancient Rome)? No - and such a story would creative a cognitive dissonance. But even more fundamentally, is there really no way I could tell an interesting historical Rome story without those inconsistencies?
