By not giving more tools to turn these great character concepts into great campaign villains, WotC ends up sabotaging the "story" aspects of their adventures. Strong DMs don't have this problem, but even then, I think a strong DM would be better served by more robust villain tools than what we get now.
That ‘sabotage’ is deliberate. WotC knows that the majority of DMs run homebrew worlds and that what they really want are modular set pieces they can cut and paste into their campaigns.
Therefore, their big hardcover adventures are really, at heart, modular set pieces with a thin veneer of story laid on top that gives them a theme, which makes them more easily marketable. (Hence why even the compilations have unifying themes.)
Case in point: STK has a thin plot about rampaging giants being stirred up by a dragon in disguise. Ignore that and what have you got?
An interesting starting town that could really be used to kick off any campaign.
A kooky cloud giant wizard’s flying tower that can be used in any campaign.
An interesting lair for each of the five main giant types plus an ancient giant temple and an ancient blue dragon’s desert lair.
A mini sandbox full of little encounters
Three well-fleshed out towns (Bryn Shander, Triboar, and Goldenfields).
A riverboat casino with ties to an ancient kraken.
And so on!
Another example: OotA is ostensibly about demons rampaging through the Underdark. Ignore that and what have you got? A sample drow city, a sample drow prison outpost, a sample duergar city, a sample haunted deep gnome town, a corrupted myconid grove, a sample kuo-toa town, a sample Underdark trading post, a magical library run by stone giants, procedural rules for traveling through the Underdark, plus a bunch of other cool encounter locations.
All of that stuff can be cut and pasted with minimal fuss thanks to the thin veneer of plot. As annoying as it is for those of us who actually want to run the stories these hardcovers present, if their plots were thicker, they would be harder for the cut-and-pasters to ignore. It’s done this way on purpose.