For the record, I was gonna watch the movie (for a chuckle, but hey) prior to Mewtwo's announcement, having been impressed by the Keldeo movie beforehand, and I take pride in assuming that fellow fans would have done the same, whether because they do give things a chance or because "hey, that killer from another time period is here, and shiny"...it's just that also prior to that announcement, people often speculated/desired that Team Rocket's greatest creation should battle Team Plasma's, and when it really was announced, fans thought they were gonna get that. Heck, on GameFAQs, I made the speculation that turned out to be spot-on as to how Mewtwo would return in the Genesect movie if it happened. Granted, the reveal was in a trailer, but still.
And the original Mewtwo coming back wouldn't have been a stretch, for other companies had been doing reunion shows/works over the last few years. Sonic Generations, for example, brought back Classic Sonic as he was, acknowledging that history as well. When Red Gorenger came back in Gokaiger, did they pretend it was a different guy? NO- they acknowledged it was the exact same guy from before. Same goes with Power Rangers for Once a Ranger, where in addition to four near-recent characters, they brought back a character from (around) 15 years ago in to fight a new, yet familiar threat (hmm, that sounds familiar...) and kept his history intact (...never mind, lost it.) Heck, the Pokémon anime itself brought back Charizard, and surprisingly went the extra mile to re-explain his backstory.
And even outside of reunion shows, Pixar released Toy Story 3 10+ years after Toy Story 2, yet didn't reboot any characters figuratively. Did the movie suffer for it? No! Because they had respect for and faith in their audience, respecting the older audience, and showing faith in the newer audience getting up to speed!
And yet it's OK that they just made up a character who looks like another character instead of bringing the actual character back, even in light of the many complaints/negative asides made about it, and even in light of the fact that in Japan, Mewtwo Strikes Back and Mewtwo Returns were re-aired specifically to get newer audiences caught up on Mewtwo's history (which also implies that Oriental Light & Magic didn't bother to tell the TV broadcaster about the change)!? ...well, it isn't.
All I can say is that hopefully, OL&M learned from their mistake for future movies.