I had three choices at the end. I chose the one that made the most sense for the character I had taken through two other games, who was all about allowing people to be what they were, and believed that sentient machines had the right to live as well. Not sure what I think about the ending. I didn't hate it with the heat of a 1000 suns like some people did, but I didn't love it either. I chose Synthesis. I'm not bothered about the relays. If the various races understood the technology, they can probably figure it out again, though that might take many generations for the shorter-lived races. But, on the other hand, if they are part synthetic now, maybe they will be able to figure out stuff more easily. It was satisfying to shoot the Illusive Man, of course. And I liked that they gave him a great last line.
But I guess Shepard is dead, which is a bummer. But I suppose if they one day want to continue it (doubtful), the ambiguity means she (or he) could come back in some form. In my game, her last memories were of Joker, Anderson and last Kaidan, who she romanced in 1, stayed true to in 2 and was with in 3, so that was nice.
I agree, I sort of didn't understand how the Normandy was outrunning the blastwave, and then at the end Joker and EDI came out - Joker had green tracking on him, as did EDI, so I assume that was genetic code re-writing itself. The last person to come out was Kaidan, so that was WTF... I had him and Garrus with me at the end, because that was how I ended ME1, with those two.

So after the credits, there is that little scene with the grandfather and a child, talking about The Shepard, so I wondered if the Normandy stuff was just a mythical part of the story.
I am glad they gave me a chance to say good-bye to characters, both my current crew and the ME2 folks. I was amused, the only one I couldn't find was Kaidan, and he was the one that probably had the sappiest dialog too.