The first pokemon movie can be broken up into three different versions. The original japanese (known as "director's cut" in the U.S.), the 2D US version, and now this new 3D "Evolution" version.
The original japanese version has the most developed story and mature moral. It includes a 10 minute prologue to develop Mewtwo's character and motivation. Through this Mewtwo's ending monologue about the 'circumstances of one's birth' has a much more profound meaning.
The ported 2D U.S. version cut out the 10 minute prologue and tweaked the storyline to give it a paradoxical moral conclusion that 'fighting is bad'. Its one redeeming quality is that it added foreshadowing by including a legend of pokemon tears to make sense of the climactic finale.
This latest 3D "Evolution" version plays off the 2D U.S. version and further degrades the story. The most jarring story change from the 2D U.S. version was the removal of the pokemon tears explanation. This version also adds 20 minutes to the runtime without adding any depth. The extra dialogue mainly comes from stating the obvious which the audience could already deduce and the other scenes added were just panning shots. It was interesting to see the movie in 3D, but it was also a bit odd as at times it felt like a claymation. The worst, though, was that a lot of the emotion and visual intensity that was put into the 2D version was lost in the 3D version. For example, when Ash was being hit by Mewtwo's pokeballs in defense of pikachu, I felt like I was watching rocks being thrown at a limp sandbag; dull and lifeless.
In conclusion stick to the original japanese version or "director's cut". It has the most fulfilling story and feels the most heartfelt.