So what is a sophisticated puzzle to you?

I've played games that have puzzles like: you come to an eagle shaped hole in the wall, you have in your inventory your pistol, bullets, and an eagle shaped crest.... Gee I wonder what you should do?

I've also played Professor Layton which is basically a compilation of Mensa style brain teasers encased in cute stories.

Do either of those games qualify for good puzzles?

The myst series that gave birth to the point and click games, games like Grim Fandango, Siberia, and the Phoenix Wright series, they were critically acclaimed, but they have their fair share of "pixel hunt" and red herrings and puzzles that require multiple approaches to solve, so does that mean they have bad puzzles?

Good and bad are so subjective to the user. If you don't find it fun, I feel bad for you because I too find certain things unfun. But it doesn't mean the game is broken or needs fixing