Well that's interesting, the deleted scene humanizes Mewtwo and the movie is so short that it wouldn't hurt at all to add stuff. If you are adamant that you want it to not drag on for too long then remove other stuff such as the pointless opening scene with that god awful 90s pop remix of the Pokemon theme (Which you should probably remove anyway). The movie should be serious, a proper anime film.
In the Japanese version it feels like an actual movie, the editing is much slower paced rather than the breakneck speed of the american version. You don't have to do the who he is constantly but at least give Mewtwo a backstory, a reason, and make us feel for him. Just because it is a Pokemon movie doesn't mean that the normal rules of character development don't apply.
Ok about him being betrayed twice, in the lab scene he basically just kills them all in seconds because the little kids need some action, it would be much better if after all the scientists have shaken hands we cut straight away to Mewtwo in him armor talking to Giovanni. Also when he is training it would be better to remove all Mewtwos dialogue to make him seem like a colder and darker character.
I think you should remove Team Rocket from the entire picture, the do absolutely nothing and there role is just to be Jar Jar of the Pokemon world.