Ok I tried to ignore this and not nitpick but Im too much of a fan of this show to watch this go by. Sic, your first suggestion was probably the best, but I would change it to having Amestris being at war with another country. One that is trying to take over Amestris, with this one being a country that has their own form of alchemy. I would say that the second idea is good, but there are only two homonculi left, Envy and Pride. And Envy would be the only one who would know what had happened as Pride was turned back into a baby. Also Envy is under lockdown and wouldnt have a way to escape.
OK, fanboyism over.