The director came out and said this on a blog before the anime aired:
Hiroyuki Morita, who directed the anime, wrote in his blog that he dislikes the original story and has, in some ways, been making changes to the plot for that reason. He also wrote that, at one point early in the development of the show, he asked manga author Mohiro Kitoh if he could find some way to save the main characters the kids who must pilot Zearth. He wrote that Kitoh responded that his choice was fine as long as the changes did not involve "magical solutions" to the story. Morita closed out the blog entry with the statement "The director of the animated version of Bokurano dislikes the original manga. From here on out, you can't expect the animated version to expand on what you might find appealing in the original. So, fans of the original, please do not watch the animated version from now on"
Fun fact Jun's battle was on their earth in the anime, so that scene/battle of his from the manga is gone along with other major things changed.
