Hence, the username 'Thought.'
Kinda a lame idea, but my first thought was that the resilient little Time Devourer, although what was left of it physically had been destroyed, the last of its essence had been spread among choice people for 'safekeeping', sort of. Lavos would have trusted the remainder of its essence to these people (human, Mystic, any others that might be put in), knowing that at least one of them would be able to utilize this power and amplify this strength, whether it would be done by killing the other possessors and taking their 'gift', or by simply gaining strength through more mundane means. Either way, at a certain point in the storyline, regardless of how strong they are, the essence inside of them would begin to rebel and take over the possessor, becoming a new being with at least most of its power back, and it wouldn't be until then that they would have a chance to actually fight Lavos, since it wouldn't have bothered showing itself until it deemed the time was right.
Just to make things easily familiarized, the 'gift' would have been spread throughout time, and there would only be a couple people at most for each era to be 'blessed.' Maybe something like Ayla's grandson, a lone shepherdess from the Middle Ages, a sailor and a mercenary that are from the present, a technician from the future, and a medicine woman from the Dark Ages. Obviously, time travel would be involved, considering the fact that there would be people from all those different eras, and it seems to be a favorite thing of Lavos's to mess with time anyway. Given that you could also choose to either let the other 'blessed' ones you meet to live or kill them, there would be an almost infinite amount of endings, especially if you were given the choice to play as one from whichever timeline you'd like.