Thanks - my problem with "canon" of Star Trek is that there was so much stuff that TNG, and then ENT (What a hack job that was) butchered - and I've never liked the fact that TAS is considered non-canonical. It had all the actors, writers and producers of TOS but just in animated form. But I digress. I also thought FASA was handed a raw deal too, but I didn't own the licenses, so, you know....
I wouldn't say that TNG butchered anything.
Yes, after TOS and TAS, lots of novels wrote lots of things, FASA made their RPG. A lot of what was made was awful. To expect Gene Roddenberry (notorious egomaniac, there I said it) to accept the huge volume of (often contradictory) information produced would be asking the impossible.
I used to read Trek novels, but they were not even internally consistent among themselves. On rare occasion, the events in one would reference another (like the idea in "The Lost Years" that Kirk was offered the Admiralty as a public relations ploy after the Rittenhouse incident in "Dreadnought"). All those materials were fun, but internal consistency was often minimal.
Other novels introduced huge WTF moments into Trek if they were canon, like Prime Directive, which has Kirk et al. Dishonorably Discharged from Starfleet and publically shamed in the Federation press for the genocide of an innocent planet, the Enterprise-1701 crippled and mauled, and introduces an invincible planet-sized world-eater that is older than the big bang and at the end has Kirk et al. reinstated, parts meant to build a whole new Constitution class ship used to completely rebuild Enterprise (less than a year before the end of the 5-year-mission and the complete rebuild at that point), and somehow in the space of a few months James T. Kirk goes from being a name on the order of a war criminal, with him having to live under an assumed name and work odd jobs (and flee in the middle of the night when his civilian co-workers find out who he is), to a celebrated starship captain being promoted to Admiral.
Basically, there was an elaborate fan-canon "fanon" created starting with the Franz Joseph blueprints and technical manuals, and there was some retconning of things that may have been assumed (pages from the Star Fleet Technical Manual were used as bridge graphics in Star Trek II and Star Trek III), but those graphics were probably inserted by production people who didn't write the scripts or produce the films.
Most of the FASA trek stuff was before my time, I only got their TNG supplements, which, truth be told, were pretty strange, like saying the Enterprise-D could travel at 100,000 C and go across the galaxy in one year, or the seemingly arbitrary ways that just about every important technology in the TNG era was invented by a descendant of a guest star from a TOS episode, or assuming that the Enterprise-D's saucer is capable of separate warp flight and its computer core is fully sentient and must consent to the Auto Destruct sequence, that the discovery of Data plunged the Federation into chaos because children throughout the Galaxy were afraid he'd steal their mothers in the middle of the night because he doesn't have a mother (seriously, they have a transcript of a Federation Council meeting discussing his discovery where they say just that), and that a Betazoid can telepathically/empathically sense the mental state of the main computer.
Tightly integrated canons like Babylon 5 and Star Wars are a newer innovation in Sci Fi fandom, an outgrowth of the horrible mish-mash of Star Trek canon, and one person overseeing things. Roddenberry did oversee Trek generally, but was "promoted upstairs" at various points by Paramount to keep him out of the creative loop after the relative fizzle of Star Trek: TMP and the first season of TNG, and the changing of who was running things meant that things were prone to change without notice. At least in Star Wars, George Lucas has been in control from the beginning, and as soon as people started to want to write spin-off novels and materials after the first 3 movies were out, they made an active effort to coordinate everything (most famously, Timothy Zahn was shipped a box of West End Games d6 Star Wars RPG materials and told to coordinate with them). In Babylon 5, you have the very hands-on (some would say micromanaging) JMS on top of everything with a world planned out in intricate detail over centuries.
Trek never had total consistency, not even at the start. Original production memos and notes showed that it was originally supposed to be an anthology series like Outer Limits or Twilight Zone, with a starship as a framing device to cut costs with some recurring sets and characters, and if you think about it, a lot of TOS episodes are essentially an anthology episode seen through the lens of a visiting ship.
For the purposes of gaming, I just set up one consistent canon (and if it violates official canon in places, so be it, as long as it's consistent within the game). To help players, I typically write up a brief guide that states any extensions/extrapolations or any materials I am ignoring, to make sure we're all on the same page here.
