Well, like I said, Probert did some sketches to illustrate Trumbull's idea and go beyond what he suggested, and these are reproduced in a few places like THE ART OF STAR TREK, so maybe you saw them there.
My initial response to the movie was largely the same as yours, except a LOT more negative -- way too much of a s-l-o-w ripoff of THE CHANGELING, when I'd been hoping for BALANCE OF TERROR, or maybe THE IMMUNITY SYNDROME (that's the one with the big amoeba, but more importantly it is very character-centric on Spock and the Doctor, PLUS reuses the great music from THE DOOMSDAY MACHINE.)
My shorthand perception (which actually ignores a couple of my favorites that aren't typical eps, like THE EMPATH and RETURN TO TOMORROW) of good TREK was, "ship fires its guns and Kirk gets his shirt ripped' and TMP had precious little of the one and none of the other. I was so ticked off I didn't even let myself get seduced by the cloud visuals, which in retrospect were some of the most beautiful shots ever attempted back then, but my positive takeaways were primarily just the Goldsmith score and (most) of the miniature work, which I still think is just gorgeous, especially given the time pressure involved.
Don't know if you're aware, but a redshirt -- well, a helmeted security guy -- did get zapped in the rough cut, when the glowy thing invades the bridge, but Dykstra's group couldn't get the whole sequence done in time, so they dropped that portion, which happens before the probe wanders around the bridge and buzzes Chekov. It was the only time you'd have seen somebody shooting a hand phaser in the film, since the other scene, when Spock shoots vger antibodies that are mistaking Kirk for Rachel Welch, also got thrown away when Trumbull came in and started fixing the mess that was left for him.
Ah, the coffee finished brewing!
Yeah, I didn't go back to see it a second time, and only watched it casually when it hit HBO. From a writer's standpoint the film was a departure from the TV series, and rehashing a monster episode probably wasn't the best choice. The movie felt more like a studio trying to play catch-up with another studio's film.
Then a year later "The Empire Strikes Back" hits the screens, and in retrospect I wonder why a Trek feature film couldn't have that level of energy. I mean to me, again in retrospect, it seems like Lucas and Kirschner out did Trek at its own game ... going to a snow world, a massive memorable chase sequence in space coupled with a little bit of laser fire, visiting a jungle world, and going to a city floating int the clouds (which I think both Trek and Flash Gordon did in previous TV and serials).
But yeah, I mostly liked STTMP's model shots. There's one or two that have me scratching my head. There's a shot where the Enterprise comes within 500 meters of V'Ger, and the POV shot you see of the bridge crew looking at the screen shows some out of focus stuff for the V'Ger miniature. Given the sterling Enterprise shot I wonder why that was out of focus. There's also a top down shot with some shotty matte work as we see the Enterprise traverse that same section of the alien....more of a lab issue, but I wonder why they didn't clean that up.
I think the story concept was okay, but that film maybe needed more Klingons, needed Kirk and Crew to beam aboard and get into some fisticuffs and fire fights with V'Gers energy-probe crew .... and maybe another space battle or two along with all of the high falutin stuff about humanity evolving with machines and saving the Earth. Just my inane opinion here.
And yeah, the extra footage in the "special extended" edition doesn't add too much.