this is just my idea, not sure:
regarding is neo really mwu or not. ... i think he's not mwu. im not so sure. but, check gundam seed, i mean the 1st series, near the end when rau tells mwu of who he is... i think this is the one that will explain who neo is. I remember rau saying he's the defective clone of mwu's father. and, there's this scene that mwu's father is asking the real father or kira, the doctor, to clone him, and after cloning, the father of mwu said that take care of the woman's child, i think he meant mwu there. and don't let him be like that bastard... he meant rau, and the last clone must have been neo.
rau is a defective clone of mwu's father
mwu, being a natural, is his father's son
neo, then is the success clone of mwu's father
pls correct me if im wrong, i stand corrected, but this is just an idea though
as for rey, i don't have any idea where he came from
but i really wish neo is not just a clone though, but i think its impossible, since the strike gundam where mwu is was pulverized by the beam of dominion in the end of seed...