I had the same end. I believe its because we both chose to borrow the spear from the guy in the SW corner when we went to do the mineral quest earlier on. If you go fight croc boss and lose, you lose the spear and he holds you accountable (this was stated at an earlier point in the thread).
If you wish to move beyond this point or see different ending besides those 3 particular ones, dont fight the croc boss, dont borrow the spear, or at least win the fight so you dont lose the thing.
For what my bits are worth, I enjoyed the game. Overall it was rather simple to get it done, you just level a few times each new area then heal and TP spam your way through fights. IMO wish there were more CG, but for what there was it was enjoyable. Needs more Sister though!