Even though "Mewtwo Strikes Back" continues to be my favorite movie, and I'm not a pokeshipper, I do consider this to be the best movie. Regardless of what may be different plotwise between the Japanese version and the American dub, I feel that everything works perfectly in this movie- the twist on the line about "the world shall turn to Ash", Ash getting picked randomly to be the one to collect the spheres but ends up being the one the prophecy is about, and Ash's enemies helping him out and sacrificing themselves for the greater good. It was definitely Team Rocket's finest hour, and I'm certainly glad their sacrifice didn't end up costing them their lives after all. I also liked all the great lines in this movie.
It's strange that I didn't like the movie at all the first time I saw it, because I couldn't understand it at all (that's part of the reason the first movie is still my favorite, because I liked it right off the bat), but over time I've really grown to appreciate it.