Those are both two great books.  In order to compare the two, don't do a plot comparison.  That won't work well.  The best way to compare two seemingly very different books is to compare their characters and/or themes.  You could compare Ender to Pi.  Both are young.  Both are male.  Both boys are very much on their own and depending on their own skills.  I realize that Ender is surrounded by people, but he is emotionally separated from everybody, and he knows it.  

Thematically, both books are about struggling to survive in the face of insurmountable odds.  Both books highlight the internal conflicts raging within each boy.  Ender struggles to come to grips with the realization that he is being used to eradicate an entire species.  Pi struggles with the will to live day in and day out.