reading through this gave me some ideas and also, I wanted to say some things that I think could be possible, starting with Bareshade stuff. Spoilers? maybe I'm just throwing theories out here.
I think it is actually fully possible to be that it's the alpha because he isn't cured, that means he can't become human and also since he has been a werewolf for so long, he is most likely going to be like Caleb just not yet cured and prolly insane or feral, I'm saying this as we have seen Bernard and Caleb as werewolves during the day. Bernard at his hut date and Caleb as... well Caleb.
then the rat's storyline, I don't think that the path is to Tao's home. I remember him saying something about him arriving here via boat I think and that the rat place was an island he found and wanted to explore out of curiosity, but I do think the path is going to be something involving Tao's storyline and quite possibly involving those ruins and the mysterious symbols we find around and in the rat king's box.
then Werewolves, I thought it was prolly Hishh or someone in the swamp, it being Ruben feels strange. like I absolutely think he would, due to how he Seem's so far, but I don't know about him traveling THAT far without us saying something that gave him an idea. also, where would he learn about Werewolves other than us? unless it's common knowledge to everyone in Aigran that they exist excluding Bareshade I don't think he would have previous knowledge about them, nor would anyone at all. Then talking about the Alpha, I agree we will prolly cure him, but I don't know how because we would need something close to his previous self to bring it back, and no one knows who he is. then the permanent cure for Logan depending on choices, I don't think it's that close at all. This storyline feels like it wouldn't be a good time to introduce the true cure due to several factors, like where would we get it? why does the swamp hold the true cure and why doesn't the witch know the true cure? and if she does, why did she give us this version? does she need Logan and Bernard like this for some reason and so she gave us that cure for her own later benefit? also I think that the tree in the misty abyss has something more to do with this because of its previous actions that make me believe it's alive and has a will of its own.
next on Lizards, pretty much everything you said makes absolute sense. like yeah, the good ending will most likely be curing the corrupted lake and saving the last of corrupted and defeating Hishh. but how is the question, would we have to team up with Othra and Xer to create an artificial cleansing water? or would Othra or someone else learn some purifying magic and Xer/MC would either team up or MC alone would need to protect them while they cure the lake? then what happens to Hishh? what happens to all those who chose to stay corrupted? do they become Exiled, and official banished or do they get like executed or something? also choosing Xer's path is going to be tough, like both would help him in adventuring but would weaken the skills together because he could always focus on one rather than the other and become better than ever. such as if he became an alchemist, he could gain incredibly knowledge and help the player by hypothesizing with them and making new powerful potions or helping them in situations requiring smarts rather than brawn or being a slut, but in the other end Xer could become incredibly strong and maybe even surpass Rhot and Grushk if the MC works with him and trains him in their ways and eventually, he could become more confident and stronger then maybe even more dominant with his personality due to his strength increasing and him getting an ego. MC could prolly keep it in check by beating his ass but if he ever won it would prolly be a MASSIVE ego boost for him. also, yes. dates with Rhot/Grushk sound like the best thing ever. I wanna cuddle with them and show them love until I die.
onto Ste and Northcrest, yeah Ste's storyline has quite a few ways it could go, like maybe that weird rat thing isn't involving with the nameless like me and nonsense though but actually related to something in Ste/his wife's family? or as you said taking us to his home to see it.
then Viccoria yeah, I know nothing on her so I'm just going to skip this bit as I don't know anything other than she hates Feliar lmao.
then Feliar, his name quite literally has liar in it. yes, he has to be hiding something, however whenever we find it out, I'm not gonna lie I'm sticking with him cause I'm HEAVILY biased towards him. whatever it is he is not leaving me lmao.
and the shapeshifter, I think it's Jester. like he seems WAY too carefree, and people seem to be after him while he has someone to protect him, which actually would be a good idea to take that shape because Scar will protect his brother and he doesn't need to worry about being found out. or it could be the father of Scar and Jester, or it could even be Scar himself and that's why he trusts no one. who knows!
the Crystal guys I literally loved them right away when they first came out so like I'm waiting on them to be updated lol. which I also have no theories for them sadly too.
then Orc's. yeah, we are most likely going to need to find Korg's clan and convince them to join us, be it legit or by... other means. then after we beat the ever-loving FUCK out of the SkullBreaker horde we find out everything and see if it is our teacher and save him if he needs saving or exile him if he was just evil the whole time and at least finally get an answer to where the fuck he went. but I also like the idea of us beating there ass' so hard the Warchief respects us, which made me kinda wanna see him become interested in MC if he fights with honor and win's because that would be kinda funny seeing MC either be flattered and say fuck off, give in and be interested or just gain a kinda weird stalker. however, I don't think they would help clear the caves, they aren't a clearing people, they fight, and I think we could just solve the issues and Northcrest could clear the caves up, which would prolly make Dulrig like you a lot more.
now onto Mythshore, as someone who has done that storyline up until its latest update, no. I don't believe that the shapeshifter's were the ones who fucked up Mythshore. if anyone did it I'm going with it being the actual family or Ruben because he seems like the type to do that. plus the place said it was a group who claimed to be able to help them, which I think if Ruben showed up they might believe him due to his reputation and he might not think he could face any repercussions due to the entire town dying according to what he already knew. I do believe the idea of the Bentley family having some extra secrets and thus being extra secretive and that they had the most power. the reason I think that is because I think they knew about the other houses darkest deed's and they could snitch and get rid of anyone if they wanted, so the other families came up with finding the shapeshifter's or the shapeshifter's themselves found that out and decided to take over the family to gain the most power the fastest and failed as they mostly disappeared and now need to find them so they can get rid of them or use them to find the secret's and gain the power the family once had.
the Paulo and John thing would make a good amount of sense, they played games already and now they just do it in a new home, so like they might become fairly popular fast due to it as well, which could be the reason other villagers join in?
then siding with the hunter, I'm not gonna lie i think Bernard and Caleb might get upset but Logan might also try and join because of how much he hates them and end up switching to Werewolves if your too hard on them and make him feel like a bad person for being one. then idk maybe the hunter could be like a bad or a good guy.
now, rat's again. yeah this could be a good idea, maybe you could "offer" to take Tao's place and be his slave and just wait until he's asleep and try to sneak off on your own after a bit and they could find you and be happy to see you as one path, the other could be sneak them both out during the chase event with similar mechanic's to the Lizard hunting event but not limited in steps because of RNG, that would make it insanely hard if you think about it, maybe instead you could have limited encounters before the rat's notice something and alert the king, which could lead to a boss fight against him or you "distract" him and they escape and he decides to like chain you up if you lose to replace his newly lost prizes and it could end up as a bad end? and if you win you could leave but lose rep with him, or if you win sexually he could ask you to come by again and instead of losing rep he remains neutral but he could become more active during sex because he is becoming more pent up without Tao and eventually if you do enough things he could just like kidnap you permanently if your too subservient and then you would either get a bad end or just lose some sanity and eventually be let out because you refuse to do things, the bad end could be left from not having enough sanity to resist and just doing as he asks and becoming his slave or something. however, after the successful instead of failure as i described you could invite Scrap and Tao to live in your house with Korg or you could invite one and let the other live in Bareshade or invite neither and let them live together in Bareshade, maybe they could offer you something as a reward for what you did for them? and depending on your relationship with the rat's they might even do something lewd because they believe you would like it? like Tao might undress and offer himself or Scrap might take the lead and screw you because of how you let him have fun? maybe Tao could learn some more confidence from Topping or Scrap could enjoy being a Bottom from learning submission from Tao?
then on the topic of the Crystal homies... yeah, a cave under our house to reach these other areas sounds AMAZING to be honest but would be weird to explain to Korg why it leads to Viccoria..... also what if she came to visit and Korg freaked out? or she tried to kidnap him again? conveniences always come at a price ;-;
and I think that a response to everything you said, at least everything I could answer, I understood what you meant and could see plenty of logic in what you said since you wrote it incredibly well! if I misunderstood something though, please tell me so I can fix it and see what happens to theories after that.