Everyone expected at least the ending to be stupid. But there's a fine line between simply appealing to kids, and treating us the audience like we're idiots. Especially Ash, for forgetting the first Mewtwo despite heavily implying it was the old Mewtwo when the trailer showed. He even said Mewtwo's name. The director is well aware of the existence of the 1st Mewtwo as well, but consciously went with making another.
Little kids are loud, hyper, and have short attention spans - but they're not stupid. Speaking from experience back in 1998, I wasn't stupid enough not to notice there was a huge difference between
this cool guy and
this obvious fake, when that abysmal Hollywood movie came out. And I wasn't even 10 at the time. Japanese kids are smart kids. Give them some credit.
I'm not mad or even disappointed in having another Mewtwo. In fact, I think it's pretty cool to have both a "male" and "female" Mewtwo. The possibilities there could be if the two met in the anime canon would be so much fun. But when you try to retcon the original, one of the most complex and sympathetic Pokemon ever made, then we have a problem.
This movie sounds like the Bay Transformers movies - high on action and very pretty to look at, but makes sad attempts at characterization and plot.