Pulled straight from his wikipidia page Rick McCallum offered McQuarrie a role as designer for the Star Wars prequel trilogy, but he rejected the offer, noting he had "run out of steam" and Industrial Light & Magic animator Doug Chiang was appointed instead.
He was retired and didn't want to be part of some massive multi-year commitment which even TPM alone was.
I suspect there was an additional reason; if you watch interviews with him from the time, you can see tremors indicative of Parkinson's disease.
Yeah, he was shaking quite a bit in his interviews around the time of the Prequels. Regardless, I know it's heresy, but Chiang was probably better in the overall. The Prequel conceptual art books are definitely more detailed than the OT.
He felt like he was running out of steam even as far back as ROTJ, and comparatively little of his material made it into that film.
McQuarrie made his mark with the Original Star Wars. He basically set the standard from right there and influenced the look of everything we saw in the five films that came after.
I heard a rumor that he left the production of Return of the Jedi over disagreements. Though the official story is more in line with refusal to work on the prequels, he felt he was running out of ideas and that he was rehashing everything. It was the natural progression of the universe becoming more defined with each successive film. Though I do think he would have been a huge asset to the prequels, since a lot of the design was rooted in being different from the original trilogy and creating a different universe. Nevertheless, his work remains the standard for designers and his ideas are still being used. McQuarrie will always be part of Star Wars.
The design and ideas of Lucas, McQuarrie and the rest are being used TOO literally in the Disney era. If set in the actual past of those eras that is understandable but not if they are set in a future date past that. The bizarre thing is that the movies set in that past, Rogue One and Solo, have more new design than the ones set in the future 30 years after that!
Honestly, I didn't even notice his abscencse. Great work on the OT, but no one person is necessary for telling the saga stories (GL being the sole exception, with John Williams as an honorable mention). It kinda bothers me the Star Wars Twitter does "McQuarrie Mondays." Where was GL's day of the week? Or John Williams's?
I feel like Chiang did a phenomenal job of replicating McQuarrie's style while bringing a refreshing and gleaming look to the prequel era. The Art of Episode I is one of my favorite reference books.
I think the idea is that the general public is already amply aware of Lucas's and Williams's contributions, but may not be as familiar with McQuarrie's.
I think McQarries influences went from Ep VI straight to Ep I without his direct involvment. When you look at the Art of Ep I - III books you can see how McQuarries Concepts and designs were developed further for the era set before Ep IV. And its no secret that Filoni and Lucas went heavy on concept arts from McQuarrie for lots and lots of TCW episodes. Best example is the Coruscant market place where Satin and Obi-Wan meet in secret. Rebels was even more influenced by his stuff, looking at how they even went as far as designing the characters after the McQuarrie drawing style.