Clip shows are about money and time, the two non-negotiable realities of the industry. It wasn't a "waste," it was a logistical calculation of how to compensate for the extra time and money spent on "Elementary" and "Q Who." It's like how TOS did "The Menagerie" (itself a clip show) as a 2-parter so they could get two episodes' worth of material for just one week's worth of filming and thus make up for the schedule overruns they'd accumulated. Look at all the shows that do clip episodes on a routine seasonal basis, like the Stargate shows or Showtime's Outer Limits (as bizarre as it was to do clip shows on an anthology series). Hercules and Xena were famous for the wild, crazy frames they concocted for their annual clip shows to keep them entertaining. The syndicated Superboy did two consecutive clip shows in its final season -- the first of which, surprisingly, was one of the best episodes of the series.
If anything, the anomaly is not "Shades of Gray" -- it's the fact that the Trek shows never did another clip show. Clip shows were business as usual in TV, so it's the absence of clip shows that's strange. "Shades of Gray" was just such an exceptionally dull and mediocre clip show, even by the standards of the time, that it drove the Trek producers to avoid doing another one, instead saving time and money by writing bottle shows light on guest stars and effects, like "The Drumhead" and "Duet." I suspect that "Shades" also prompted later shows' producers to try harder to make their clip shows interesting and worthwhile, whereas earlier clip shows generally tended to be quite dull and superficial, not that much different from "Shades."
