I don't really understand the meaning of that entire part, is it supposed to give the series some "authentic" feel? yup there's indeed an assassination attempt at the Pope John Paul II in 1981, and indeed there is the Fatima Prophecy, but I think this series is far too... fantasy-ish to give any "realistic" feel anyway...
So my interpretation of the possible meaning of the very end
Spoiler:
1) Aion becomes God... kinda makes you wonder why they fight so hard...
2) you can't escape the path set by God despite whatever you do... also kinda makes you wonder why they fight so hard...
3) Aion becomes the Pope... makes even less sense than Aion becomes God...
4) We shall always follow God... errr... so this is supposed to be a Christian propaganda show? I don't think so...
5) Seriously, I don't understand...
Anyway the ending is perfect up to the point
I'll have to say again, such an excellent, touching, both happy and sad, and beautiful ending.
And I agree that even a wonderful ending can't save the show from its overall mediocrity...