First off: I know this is old, but eh I wanted to say this. It's also to note I haven't read Perfect Works myself, only heard summaries of it, so there may be some misinformation in here. Where the Perfect Works story was going after Episode 5 is a bit hard to tell just because, as you said, Xenogears ended at a very natural point, and it would definitely be the climax if nothing else, but I still think the game set up to some future events a decent amount. I'm going to start with the theming, because I feel like that kind of leads into everything else. The theme of Episode 5 at least was becoming whole, I don't think I really need to explain this the game was fairly obvious about it, but towards the end it started having more themes of breaking a cycle, the most obvious being how Uroburas was the final boss instead of Deus, the Uroburas obviously being a symbol of a cycle, which to me feels like that would be the theme of Episode 6, the breaking of the cycle. Starting with that, I don't think there'd be much room for the protagonist to be another incarnation of Abel. This would obviously fit with the theme, but also, with the Zohar gone Abel has no real relevance since his powers of the contact would be gone, though I suppose Xenogears would play a part in the plot still, but it definitely couldn't be a re-incarnation. With the Zohar gone, all the memories of past lives Fei has would be gone once he died and got re-incarnated again, and Fei being the protagonist again doesn't feel likely. HIs character arc was very well wrapped up in episode 5. Really most of the plotpoints of the series going forward were wrapped up, so for who would be the protagonist of episode 6 I think the ones with room still left would be the best place to look. There are some that didn't get full cloture like Rico and Maria's stories, but I think I'd credit that more to the limited resources than intentionally writing it that way. The obvious one that still has room for a character arc would be Krelian, a large chunk of the ending was dedicated to Fei telling him that he still had time to make up for all he did. Granted there needs to be an explanation for this since Krelian kinda hitch hiked with the wave existence in the end, but there is actually 1 hint the game does have that Krelian could come back, and it's in the final shot. You can see feathers falling on Kadamony, which could just be from Xenogears, but that placement feels a bit too plot relevant to just kinda, throw it in. I'd say those were the feathers from Kelian in the ending, I'd say the plot explanation is just that the wave existence in its last moments in the Gears universe transfered Krelian to some kind of data bank within Kadamony to be revived. This could also have symbolic meaning because Kadamony could revive Krelian as a normal person, getting rid of the nanomachines, which would fit into the idea of him ridding himself of his past. I don't think anything beyond that can confidently be said, but I do feel that is the most likely outcome given what information we have. This is actually even supported by Xenoblade. Xenoblade 2 was a telling of part 5 of perfect works as well, and the game set up a very similar plotpoint to this as well, though I won't go into too much detail in case you haven't played it. So yeah, imo the most likely outcome for part 6's story would've been Krelian coming back and making up for his past sins. Part 5 would still be the natural climax, but one final more calm episode could provide good cloture to the story.
