I don't understand this urge people have to some kind of duty the mangá/anime has to explain EVERYTHING in it. Please, stop it. Maya and Alethia were created, you can either consider it being a creation of nature or a supreme being, it's up to you. I don't see how it could've been better if the author explained this, unnecessary.
As for the entire mangá, I loved it and for me it's one of the best of all time. Most people did not accept the deaths, but deal with it, life in Eden or reality itself is shitty like that, there's not mercy or absurd plot armor. Ennoah at the end fullfilled his part in the world, I don't see why the need of keeping him alive. As for Kenji and Loji, they have much to evolve and mature.
I don't have an exact opinion about the jokes, Elijah and Miriam should live grieving and suffering? I just think that's not the point in Eden. Sophia is one of the most interesting characters I've ever seen, satisfying to see her leading the colloid to another universe.
10/10