GNR Fatman: The fatman is the result of a scripted event. If you did something to cause that script not to run, neither the soldier nor the fatman will be there. You could call this a bug if you want.
Scientific Pursuits: If you're talking about in-game quest completion credit, I don't think it's possible to complete Tranquility Lane without completing Scientific Pursuits (assuming you've successfully started Scientific Pursuits). But if you're talking about the achievement/trophy, that does appear to be buggy.
Behemoths are easy to kill btw use the dart gun and put it on very hard own them with missile bottle cap mines or chinese assult rifle :D.
Don't worry about the Fatman(especially if you managed to kill the Behemoth without it) there are at least a dozen in the game. Close by in the Capital rotunda, Whitehouse Basement, are a couple. It is a cool weapon, but not really useful.
Also, I wouldn't worry about completing all the quests, you will want to play the game again as a different character and that will give you the chance to go thru again and do things different. This is the beauty of this game. You can choose to travel your own path.
Likely, you missed something along the way and the quest completion was not triggered. In the GNR, you need to hook up with Sara Lyons before you get to the GNR square, then follow her group to the square, this is when the Brotherhood guy gets it by the fountain. Be sure to let the Brotherhood lead on this, if you kill all the mutie's, who's going to kill the guy with the Fatman?
Scientific Pursuits--make sure you talk to Dr. Li in Rivet city before you go to the Jefferson Memorial.
I cant really gove you an answer,but what I can give you is a way to a solution, that is you have to find the anglde that you relate to or peaks your interest. A good paper is one that people get drawn into because it reaches them ln some way.As for me WW11 to me, I think of the holocaust and the effect it had on the survivors, their families and those who stood by and did nothing until it was too late.