Some possibilities that occurred to me that I didn't see (Or maybe didn't notice) in the original list or in later posts.
Protect>Spiky Shield. There is literally no disadvantage to Spiky Shield.
Arguably Play Rough>Light of Ruin.
Air Slash, Air Cutter, Gust>Aeroblast. (Or Oblivion Wing?)
Shadow Punch>Shadow Claw. It's a small thing, but there's No Guard/Klutz Golurk if nothing else.
Supersonic, Sweet Kiss>Confuse Ray.
Seed Bomb>Leaf Blade/Petal Blizzard.
Acid>Acid Spray? They lower different stats though.
Extrasensory>Psychic. Relevant to more Pokemon than you might think, though if you feel flinch-hax is superior this shouldn't count.
Arguably Ancient Power>Power Gem. Math-wise, if you used up all its PP every match, Ancient Power would activate less than once a match.
Metal Claw>Meteor Mash. Again, relevant to more Pokemon than you might think.
Aqua Tail>Crabhammer. No disadvantage at all.
Ingrain>Aqua Ring? Ingrain prevents the enemy from forcibly switching you, but is otherwise the same thing but worse.
Protect>Spiky Shield. There is literally no disadvantage to Spiky Shield.
Arguably Play Rough>Light of Ruin.
Air Slash, Air Cutter, Gust>Aeroblast. (Or Oblivion Wing?)
Shadow Punch>Shadow Claw. It's a small thing, but there's No Guard/Klutz Golurk if nothing else.
Supersonic, Sweet Kiss>Confuse Ray.
Seed Bomb>Leaf Blade/Petal Blizzard.
Acid>Acid Spray? They lower different stats though.
Extrasensory>Psychic. Relevant to more Pokemon than you might think, though if you feel flinch-hax is superior this shouldn't count.
Arguably Ancient Power>Power Gem. Math-wise, if you used up all its PP every match, Ancient Power would activate less than once a match.
Metal Claw>Meteor Mash. Again, relevant to more Pokemon than you might think.
Aqua Tail>Crabhammer. No disadvantage at all.
Ingrain>Aqua Ring? Ingrain prevents the enemy from forcibly switching you, but is otherwise the same thing but worse.