I strongly believe that Madame X will not be the final fight. Almost convinced actually. If anything, she probably will be our last and unexpected ally, joining at the last moment after we beat her and prove our point. She clearly showed she is not interested in senseless destruction, she is concerned about safety of timelines, and she clearly knows more than most of the characters. And obviously she's got a good reason to do things she does.
A agree, however, that Crescent feels some sort of guilt or responsibility before the MC. One of my guesses, is that it was her, who inserted The Interceptor into the MC, forcing us to take over his body. Or it was her fault MC real parents died. But i do not believe Crescent will be the final battle either. Her methods are questionable, but her morals also seems to be in the right place, and she does a lot of things to help our heroes.
My best 2 bets for main villains so far:
1) Space-Time duo. They operate outside of human morals, disregarding human lives, fates and their world for their still unknown goals. Their motivations are shady at best and also there clearly was a heavy reason Crescent, who i believe to be on a good side, had to betray them.
2) Arceus Cult, probably Arceus himself. No matter how you look at it, at any point of any timeline we visit Arceus Cult is present in there in any form or way, doing sacrifices. The castle on the prison island, where presumably sacrifices from the beginning of the game were made, is also seems to be a very important place for team Xen and Madame X.