Essentially, a "John Conner", son of Sarah Conner, had to exist in order for T-1 to take place. I can be debateable as to whether the John Conner who sent back Reese is the same as the one that Sarah is pregnant with at the end of T-1. Myself, I would say it is impossible since Reese would never have gone back in time without John sending him.
That's one of my big problems with things. If it's a different John Connor... 75% genetically different... how could he be just as successful leading the resistance? He's a whole other person. Skynet already succeeded in killing John Connor by preventing his conception. I guess the new John Connor was pretty effective himself, but it makes you look at things in a whole different way.
And I've just thought of a big fly in the ointment...
How could Reese have the photo of Sarah Connor that was taken with her pregnant with his child? That photo he fell in love with? It was the same exact photo that was taken at the end of the film. That photo could only exist after he went back in time. So that would be indicative of a circular time loop... Reese was always the father of John Connor. The photo proves it.
It is possible that the events of T1 (the parts shown in the future) could have been the second time Reese was sent back in order to have the same picture, or could just be a coincidence that a very similar picture was taken in both timelines. This is a chicken and the egg quandry really. There is no reason for Reese to go back in time until the Skynet sends back Arnold. Hence, the John Conner from T2 would never have been created until Reese goes back in time. One has to assume that there was a John Conner that lead the resistance who sent Reese back thus changing that "present" time. Also, I don't thank you can really calculated the genetic differences...he would be at least 50% different to as much as 100% if Sarah happened to give him the other copy of every chromosome.
As for T4, I believe the original intent was for it to be a sequel to T3 since it appears John will be with the daughter of the General from T3. However, looking at the previews, it seems that John has no idea about the human looking Terminators. That would lead me to believe that this could be a prequel of T-1 where this John Conner was not fathered by Reese, but I don't think the dates match up, so we'll have to wait and see.
Ed
Reese only goes back in time ONCE.
I think you have the whole premise of Terminator 1 messed up. Here it is in a very short nutshell.
Some where in the future - Skynet is loosing the war, they are on the verge of defeat. They send T-800 back in time to kill Sarah Conor the mother of John Conor to keep the leader of the resistance from ever being born (not realizing the Grandfather Paradox, being that if they don't do that Skynet will never exist).
T-800 fails it's mission and is destroyed in a warehouse of Cyberdyne. Reese's one night with Sarah results in the conception of John Conor. Picture taken in desert, that picture survives on to be the picture given to Reese in the future by John so that way he knows what Sarah looks like when he is sent back to save Sarah.
1997