EDIT: many of the details in this post are due to be updated based on new information discovered in the E3 footage. I will either amend the post directly, or more likely will provide details in a new thread a little later on.
As many of you may know, I previously made a number of predictions regarding the pre and post-war elements of Fallout 4, several of which turned out to be surprisingly accurate. Now, based on what we have seen so far at E3, I believe I may have stumbled upon a big clue towards the storyline for the main quest. And it is HUGE! Please note, if this information turns out to be correct, then you may be reading what could end up being fairly big spoilers. Therefore please DO NOT READ if you do not wish to risk spoiling the surprise of the main storyline. For everyone else, here we go...
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In the concept art we saw at E3, we see several groups of images with a larger image in the centre. Part way through, one of these larger images shows us what looks like a ghoul pirate. A few shots later, we are shown another much larger group of images, and then there are 43 further images shown in quick succession, the 43rd one being the pre-war shot that Todd talks about. It's the images in this section, two in particular, that I want you to focus on here. The images in question are the ones in the 37th and 39th shot:
37: We see our protagonist, accompanied by his dog, and he is firing a mounted milligun from the side of a vertibird.
39: Again, we see our protagonist with his dog. This time, however, he is accompanied by a soldier in BOS power armor and the ghoul pirate we saw in the earlier image. Note the damaged airship and other aircraft that signifies a large-scale battle.
Also, in the footage shown at the Microsoft conference, we enter the "Museum of Freedom" to assist a small resistance group, which according to the leaked casting documents are actually the Commonwealth Minutemen. (EDIT: Changed this reference from Railroad to Minutemen as per casting document)
But what does all of this have to do with the bigger picture? Here is what I think happens:
If this turns out to be true, then the real twist in the story would be this:
Edit: the ghoul pirate theory may end up being a red herring, although I do feel that he plays a very big part in the events of the main quest. If this is the case, there are still several other possibilities that involve the son and possibly even the mother being alive post-war.
As an interesting side-note, here is one more idea for you to consider: