Well it's not even true that they don't want you to do two puzzles to get a shrine. I can think of a bunch of shrines which have puzzles from a quest leading to the shrine and the shrine still having a puzzle. So it's not a hard and fast rule. I don't mind blessing shrines when I solve a substantial overworld puzzle like the 7 heroine statues or the labyrinths though. What disappoints me is when I feel the puzzle wasn't that challenging. The one where you follow the champion statues in the desert was a bit too simple. And I -just- chanced upon a blessing shrine today which wasn't connected to a shrine quest (maybe I didn't get it yet?), just from exploring and then bombing a suspicious area on a cliff. Would have definitely preferred a puzzle there.
Worse are the tests of strength. Just pains in the ass.
I dunno, I really enjoyed some puzzles, but overall BotW is a disappointment on that front. A lot of the puzzle shrines felt like tutorials for a bigger puzzle that never came and I often got to the end saying "that was it?!" There were a handful of shrines that were really good. I wish they would release DLC packs of good puzzle shrines that increase the complexity of the puzzles.