Hence why I think they should have been more explicit about what went on with Isobel's soul, since they seem too imply setting weird but leave it unanswered. As for why bring back the dead, he's the chosen of Myrkul, whose whole thing is necromancy and bringing back the dead. It makes perfect thematic sense why he would resurrect someone rather than pick someone already living. I think you're missing the forest for the trees here a bit; there's nothing about the current villain set up that inherently can't work. The problem is that Larian put it all together badly. The problem is so few of the individual elements and strings of this game we've together, resulting in a story that feels messy and overcomplicated when if you lay it out, it's not really got that much of consequence going on.
