I'm not even going to mention the ending aside from this sentence. Too many things there to list.
David returning as a main villain. Do something better with the auxilaries, the Yeerk Peace Movement, and Loren. Or just leave Loren out of the later part of the series altogether, as she seemed to serve no real purpose. Maybe give Cassie her own unique battle morph, and not make her the special pet of the series. Not have one of Rachel's sides overshadow the other, since her having two sides is what I like most about her character. Make Mellissa a more important character. change the Megamorphs so that three out of four don't deal with time in some way.