That's true, but he hasn't made a concentrated effort to insure that material is ignored or overwritten. At worst, he's said that some of the stuff dealing with the timeline outside of the movies doesn't reflect the way he would do it, but it's still a valid way. Lucas has also included small nods to the EU in the films.
Actually, onscreen "canonical" ST has included numerous nods to the books and comics.
F?ranz Joseph's designs, floor plans and ships' names, classes and numbers.
Diane Duane re-used her premise of "The Wounded Sky" in a TNG episode, but her female "glass arachnoid" alien scientist became a seemingly humanoid male Traveler.
Alien sketches from the "Starfleet Medical Reference Manual" in DS9.
Sulu's first name (ST VI) came directly from the Vonda McIntyre novels.
The popularity of Konom the turncoat Klingon in DC Comics post-ST II comics possibly helped to inspire the concept of putting Worf into TNG at the last minute. Certainly, fans used to quiz GR about Konom at conventions.
Several episodes have included salutes to TAS.
Bottom line is, no matter what aspects of the EU different fans like and dislike, they don't get into arguments over it being part of the continuity.
They don't? I doubt that
very much.
How did they handle the SW comic where Jabba the Hutt was introduced as a fat humanoid? If SW tie-ins routinely inform the series, Jabba should have stayed that way when introduced in "The Empire Strikes Back".
Whereas in the Trek franchise, non-televised media is second class at best.
How is not being "canon" making the tie-ins second class?
Sure, I was hearing fans label the novels as such way before 1989, which is when Richard Arnold issued Gene Roddenberry's memo from the ST Office. I heard fans telling me they were refusing to read the novelization of TMP, because they'd heard that GR had filled it with stuff that never happens in the movie. Ditto McIntyre's ST II and III's novelizations, which had a romance between Saavik and David, a captain promotion for Sulu, and many additional characters and scenes.
No one had decreed anything about "ST canon" at that point.
Let's imagine for a moment that JJ Abrams had simply added William Shatner playing Old Kirk to the ST XI script. Only about one percent of ST fans read all the books. Shatner's novels were very popular, so let's exaggerate that
ten percent of fans have read them. Certainly, while its likely the general public caught "Generations", it's unlikely they knew to read "The Return".
So they go along to ST XI and there's Old Kirk, fully recovered from his Nexus death and
now many years older than when his character died onscreen.
People say, "I thought Kirk died in 'Generations'?"
And the answer is: "Oh, you should have read the
tie-in novel trilogy, now long out of print, where Kirk was resurrected - twice - first by Romulans and then by Borg nanites!"
I see nothing wrong with a show's creator setting up a very clear line for the stories being told by licensed tie-in novels, omics, short stories, RPB manuals and even the little cut-out character biographies on the back of action figure packaging. This material should not routinely inform the parent work. And tie-ins, which can sometimes be what solidifies a new fan's resolve to follow a series, should be an accurate depiction, at time of writing, as what can be extrapolated from the screen.
And for SW, such material also does not mandate information that the parent work must follow. As you said, Lucas has "also included small nods to the EU in the films". And you know what? So has ST's showrunners and scriptwriters.