Think the reason people hated Mega Mewtwo Y was because previews of the movie in Japan made it out that the Mewtwo was the First Mewtwo, there was even a scene where Ash says "Mewtwo!" when it blocked a blast then Mega Evolved....hinting that the reason Ash knew it was Mewtwo because his memories wasn't wiped out during Team Rocket's lake attack. then again it's extremely hard to make a Pokemon movie where a Pokemon by itself is inherently evil, rather than being puppeteered by a human, which is why Mewtwo was beloved and more memorable than other villains. the closest you get is either Zoroark...for a short time, or Molly Hale, who was less villainous and more benign, it's a kid with the reality-warping remote control.
Heck, Human villains seems mostly like "Hmm, there's an ancient/powerful/mythical pokemon with abilities here, i shall utilize them to use their power for my own purposes", but then there's movies like Manaphy and Lati@s where Villains just isn't major and the plot is just....there, presumably this is why they made movies where Pokemon are berserk and/or fighting like the Time-Space trilogy. There is the Lucario movie, but that's more like filler within movies though still entertaining on its own merit.
Indirectly the polarizing characterization and appearance of the 2nd Anime Mewtwo left a bad taste for M-Mewtwo Y....only thing that could reasonably save it now is if Mewtwo comes back for Smash 4 with Mega Mewtwo X....but for some reason Game Freak thinks Y is cooler than X, but M-Charizard X is cooler than Y. heck, MCharizard X's color scheme is similar to Zekrom's.
RSN: Plucky9, Total: 2574. KoL: Plucky, currently an Disco Bandit ACNL/3DS FC: 4897-5920-6758 Ricky/Gemiere of Farm