Riven was also a huge improvement in worldbuilding. The world of Myst was often rather contrived; the places it depicted didn't always seem particularly "lived in", and the puzzles were often rather contrived in nature -- in many cases, their motivation was simply that the world itself was created as a puzzle. The rocket ship piano puzzle falls squarely into this category, for instance!
Riven, on the other hand, depicted a much more natural-seeming world, and its puzzles fit much more organically into that world. For instance, one early puzzle involves learning the Rivenese number system from a child's toy. Some of the Moiety puzzles seem a little artificial, but even those do have some in-game motivation (as part of a security system).
They were pretty good about only putting the CD swaps only in major area transitions. Anytime I saw one of the magnetic rail trams, I knew it was time to get the disc box out and prepare for a swap.
Putting the more technical aspects aside, I found the games after Riven to be lacking something, and I only discovered afterwards (maybe even only after the second post-Riven game) that it wasn't by the original studio/team/brothers.
Uru, despite its many problems, seemed to recapture some of that magic. But I'll always wonder if that's actually true, or just because I knew the original team (or at least one of the brothers?) was involved again.
(Not that the Riven sequels were bad! I quite enjoyed Myst 3)