I have read so much about the ending and now I concluded a thing for myself.
As you can see in the game, the Destroy route is red (Renegade) and left is Control (Paragon). Let's say that the indoctrination theory is true.
If you go for Control, I don't think it's a Paragon choice. You will get indoctrinated.
If you go for Synthesis, you will die and you will not run away from indoctrination also.
If you go for Destroy, all synthetics are destroyed, but you still have a chance to survive (he/she is still BREATHING!!!!)
So, Destroy is the best choice at here.
Think carefully...
I have no idea of what will happen if I choose Control. But Shephard DIE!!! (And if the indoctrination theory is ture, this choice will not change anything)
I'm not going to let all organics to involve themselves to synthesis. ORGANICS ARE THE MASTER OF NATURE!!
It's hard to choose Destroy, because it's sad that Geth and EDI will gone...
In my storyline, I have chosen Synthesis (which I felt that it's a wrong choice), as it seems that Synthesis will provide the best ending for this story.
I will go for Destroy by restarting the previous mission.
If you think sending everyone into the Dark Ages is a good choice, then I have no words.