I agree that this episode felt a little too messy and was just packed with too many side-plots that didn't go anywhere or had enough time to breath. It is a joy as a long-term comicbook fan too see so many different comicbook storylines meshed together but at the same time it is just too much and indeed feels messy at times.
Jean Grey's Phoenix moment for example felt so random. They could at least give her the Phoenix powers for the rest of the episode. It probably will relate to Mother Askani who may send the Phoenix to Jean from the future to save Nathan?
The set up for season 2 was pretty amazing. Already like a "best of" of Apocalypse storylines we love (and hate!).
Still, season 1 was a wonderful ride with gorgeous moments throughout!!! I just wished they wouldn't have pushed too much into it and stayed with certain storylines just a little longer.