Gee, this thread is all over the map.
For the record, Khan was the first VHS tape I ever bought circa 1983 or so and I practically wore it out, so I've got strong opinions about it. I have a hard time watching it since I've watched it too much and have almost every frame and every beat of the soundtrack memorized, but I still hold it in high regard.
As a kid who say TMP at age 9 and Khan at age 12, the reason Khan matters so much is that it restored something to Trek that was lacking in TMP.
You know what that is???
What makes Khan fun? It's things like the turbolift doors opening and McCoy saying "Who's holding up the damn elevator?...Did she change her hairstyle???" Absolute perfect comedic delivery. It's like watching an Olympic athlete nail a 10. The characters were spot-on, exactly the way we wanted them to be.
And there's a problem with the MacGuffin? Do you have a problem with the Ark in Raiders? The Genesis device and the Ark in Raiders are really not that different as a MacGuffin. Both films are action romps, and both very successful and well-remembered. So why all the hate lavished at Khan? The film came out at a time when it had to compete with E.T. and Poltergeist and it did pretty well while single-handedly saving the franchise. Despite ILM, it did it on mostly a shoestring. It has a very TV or Star Wars: ANH ricketyness despite the blockbuster status it now has. Montalban shed his Mr. Roarke typecasting which was no minor accomplishment at the height of Fantasy Island. Aside from "Khaaan!" Shatner gave his most buttoned-up performance as a by-the-book-Admiral-with-a-wild-streak Kirk. Compare that to Shatner mostly just playing himself in Trek IV (effectively--for laughs) and V (ineffectively). Give this film credit where credit is due.
Trek doesn't have to be just one thing. If you're in the mood for the cerebral, Trek's got you covered. Heck, The Cage was rejected for being too cerebral, and TMP kind of mirrored the initial commercial issue with Gene's way of thinking. But TMP IS a valid expression of Trek, just as Montalban 'overacting' and Shatner screaming 'Khaaaan!' is perfectly valid, just as a flat-out comedy ala Voyage Home was perfectly valid. It's the combination of all of these things that makes the Trek franchise as rich as it is.
Sometimes fans are so fickle that the only thing they truly enjoy is nit-picking the stuff they say they love. Seriously...