I don't know if this has been mentioned yet, but I just realized that the body that is in the lighthouse that has the sign that says "Don't fail us" (or something like that) may actually be Booker. Or a version of Booker.
The "Twins" hint that versions of Booker have attempted Elizabeth's removal from Colombia and failed 121 times. Perhaps this is the most recent failure, and he's put there as a warning to our Booker.
I don't remember if he's wearing the same clothes as our Booker (and he wouldn't necessarily have to), but it is interesting that his face is covered.
I always thought the whole beginning (including the body) was just the part of his memories the brain created after traversing time and that the game actually started once he was in the pod to go to Columbia.
Really? I saw it more as a taunt from Comstock. In the future that Comstock saw, Booker had to come and he had to attempt to save Elizabeth. This gave Elizabeth hope which was what allowed Comstock to break her and brainwash her later. Without Booker, Elizabeth wouldn't have that same hope and wouldn't have been broken that way.
As Rosaline Lutece mentioned, Comstock saw this as the only future, he didn't realize Booker coming to save Elizabeth and then failing was only a possibility that could be changed.
The body was probably a Vox or someone similar put there to taunt Booker.