The ending would've been better if the writers took a page from Final Fantasy 6's midpoint. Have all the worlds converge into one, genocide and all, kill off all the Scions, and leave our characters as the survivors in a shattered, but whole, world. The fallout of such an event, and with us pinned as the cause by the other survivors, would make the next story arc a truly interesting reboot. Not to mention our characters would have to live with the knowledge that our actions caused the death of all their friends. The surviving city states from all the old, sundered worlds would quickly vie for power and limited resources.

Plus it could allow the designers to change all the classes and dungeons in a fresh and interesting way. There's really no reason a post-merging game couldn't have different class designs branching off of the "previous world" magic and martial systems.