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Flannery's hot spring puzzle because you can look at the positions and make sense of it, but you don't expect that from all the other transporter puzzles being random. Also, I like the dialog and teams from those trainers more than any other gym.
Did they upgrade the difficulty for Sootopolis in ORAS, because I used to love this puzzle and solved it naturally, but I had to brute force ORAS's. Maybe I am just becoming more retarded now.