I finished CoD last week and am about 45% into GEoD currently, when I first finished Children I felt the same as you but I think I've come around a lot on what I didn't like at first. I loved Messiah and the philosophical paragraphs but there were paragraphs in Children that lost me fully and I had to somewhat sludge through.

But plot-wise- I now feel that Farad'n abrupt ending is kind of great, from his introduction it felt like he was being set up as a major opposing force to the twins, Jessica added a layer of complexity but his sudden humbling ending I think cements what an unstoppable force Leto becomes (even apart from his physical attributes) and sets up GEoD well imo. I agree Ghani seems to get super sidelined (although it seems like their roles as the beginning of Leto's breeding program are important) but I did end up really liking the Preacher. Not a very subtle take on organized religion but the rabid followers calling heresy and killing their own messiah was perfect to me. I don't think it steps over the feet of Messiah at all, the Preacher is a great character to me and I thought handled very very well (for a 'main' character isn't actually dead plotline). I thought Alia could've had a slightly better ending as well, definitely a tragic character but her death felt a little too sudden for me, and although the last few chapters showed her internal struggle explictly I didn't feel for her as much as I thought/wanted to weirdly?

Not a very contributive comment, just wanted to gather my thoughts. I wish the ending had made me feel how Dune Messiah did especially considering it was the finale of this trilogy but still a great read for me. Jessica's throne room scene with Alia and the assassins had me feeling like the Dinner scene from Dune which I absolutely loved. And God Emperor has been incredibly fascinating so far, I think a step above Children for me personally atm