I think the main reason the puzzles are disliked is because there such a big contrast of gameplay between the outside world and inside dungeons. At the start of the game you are treated to a somewhat long tutorial, but then you finally enter the island and you can just run around blasting everything. Feels pretty great. You get the false impression this is what most of the game will be like: bright cheerful colors, fast-paced combat, hype music, just running around doing MMORPG shit with party members that have lot of friendly banter.

Then you enter your first dungeon and the fun ends now. You are isolated from your party members, no more "LASER BRIDGE!" or big nerd saying big nerd things, no more bright cheerful environment, it's all cold and monochrome, and you can kiss goodbye to running around blasting everything. There's still some enemies but you mostly just do puzzles, again, and again. They're not bad puzzles, but the problem is that the game is a 9/10 outside of dungeon and is a 7/10 in dungeons. It's a big downgrade. Everything that makes this game unique is stripped away, you want to explore the MMORPG world and uncover the mystery of Lea's identity while goofing around with party members and all of that is put on pause so you can relentlessly do puzzles which are definitely not as interesting. When the non-puzzle content is so good, the puzzle content is just an annoying formality to get done with.

tl:dr if they removed 90% of puzzles and allowed you to bring party members in dungeon this game would probably have received a lot more love.