Other than Majora's Mask, the series has had pretty lackluster puzzles IMO.
Majora's Mask is often lauded for having the most interesting investigative non-environmental puzzles (The Anju & Kafei side-quest, and Romani's side-quest immediately come to mind) and rightfully so as far as I'm concerned. It also has some of strongest theming, and narrative elements in the franchise's history.
However, it's dungeon design leaves a lot to be desired; it also doesn't help that there are only four of them (which means the weaker dungeons stand out way more than they would in a game with 8 or 9 dungeons)
Woodfall suffers from being incredibly basic, and making use of the most uninteresting mask in the game (They really couldn't think of anything more interesting than hovering towards static platforms??)
The best thing Snowhead has going for it is the Goron Mask's rolling ability (dat game feel) and Ghot.
Great Bay...is just frustrating to navigate and manipulate. It also has surprisingly simple puzzle design for such a confusing layout. Also, Gyorg is the worst.
I know we all have different opinions, but it's hard for me to comprehend why anyone would put that game's puzzle design over OoT's, TP's, SS's, or even some of the post-2000s portable games' puzzle design. Puzzles and obstacle/platform design wasn't really that game's strong suit.
Edit: It's mostly remembered for it's thematic elements, story elements, and investigative puzzles/side-quest.