Whether Manhattan project should be a small or Great wonder has been argued about a thousand times, and I think it should be...either.
I think by making it a Great Wonder, Firaxis was thinking along the lines that Russia, Germany (I think, History buffs may correct me on that) and the US were all developing the nuke at the same time.
However, I believe (once again, don't kill me if I'm wrong) that Communist Russia had a spy somewhere in the Manhattan Project, and was stealing secrets and plans all the time---giving an answer to why Stalin was not surprised when he was told about the A-Bomb being dropped on Hiroshima.
Overall, it seems in history that the nuke was developed by several countries independantly, but each was using espionage to try to keep up with each other.
I definetely think that nukes are slightly flawed in this game---I think they should kill the units they hit, not just redline them. I have no complaints about the rest of the nuke's effects in the game, but this one really bugs me sometimes.
Another Long-Winded Post