me and FE have already started threads about why they dont just destroy the machine to end it all. the simple fact is the game would be toally boring and end without any kind of last boss or interesting time compression and cool ending.
edit: ive just realized something else. if they destroyed it now it would mean what happened with ultimecia possesing everyone will never have happened and the seems as there was already a time loop destroying the time loop by destroying the machine could probly just end up with a big confusion in time and everything being destroyed.the only way it would work is travelling to the future. in simple form, mormally destroying the machine would work but due to a time loop in the game destroying the machine would probbably destroy everything else.