There seems to be one glaring difference when it comes to the Destroy, Control, and Synthesis options compared to the Rejection one. In the first 3 you see all this stuff about rebuilding and living happily ever after (except the Geth and Reapers in Destroy). Then you get the end with Buzz Aldrin talking to the child and telling stories of Shepard. During this exchange, which I assume takes place long after story, the boy seems to be unaware of other species and other worlds. It's almost like something happened that may have separated the species again after the supposed times of peace.
The reason I think something big happened in the first 3, is because in the Rejection ending we get something a bit different. It is only in this ending does the kid say "And that's why we have peace?" The woman says that yes, and it is because of everything we accomplished and were able to pass this information to future cycles. So in this ending there is peace, but it would seem that may not be the case in the other endings.
In the Control ending it appears that Shepard is no longer like Shepard. He talks of control being power and whatnot, like TIM did. I feel this option is a trap set by the Reapers and the starchild (he even seems to be a Reaper from the Rejection ending where he says "So be it" in a Reaper voice.) Eventually Shepard likely succumbs to indoctrination and the Reapers take over.
Synthesis seems to be the option the starchild favors you choosing. Here it seems to me that we are indoctrinating the entire galaxy. I feel this likely lead to a galaxy wide extermination.
Destroy also would have lead to eventual conflict because we are lead to believe that even if we wipe out the Reapers (and Geth) our future generations would have built their own synthetics and thus creating a similar situation to what we find ourselves in now.
Rejection seems to me like the best choice, and the choice that the real Shepard would choose. He has no reason to trust the starchild and it wouldn't make sense to align ourselves with the Reapers. By picking this option we will fail in stopping the Reapers for this cycle, but as we see we are able to leave behind a message for the future much like the Protheans did for us. However this time we accomplished more than the Protheans and are better suited to advise the future generations how to stop the Reapers. We could spare them the wasted time of building the Crucible.
Anyways it would appear that after picking Rejection, the future cycle does receive our warnings and are this time successful against the Reapers and have achieved peace. Thus, Shepard has fulfilled his destiny in defeating the Reapers and creating a galactic wide peace.
And when you think of the endings in that way, ME3 actually seems like less of a disappointment (at least for me.)