There are even more inconsistencies than what I had originally noticed. When they say the battle will be fought in the present I would assume that to be anytime around when Reese comes before Skynet becomes aware. So, while I think the word present is a bit flexible, obviously this fight didn't happen and Judgment day happened.
I just realized that if you ignore the events of Terminator 2, T1 and T3 make a lot more sense together. Sarah gets knocked up and gives birth to John. John grows up always hearing about Judgment say and how he is supposed to be some sort of great leader, He classifies it as BS and goes on with his life (mostly). His mom kind of gets crazier as she gets older and finally dies still preparing for Judgment day. John is devastated by the loss of his mother and starts to reconsider his view on what his mother always told him. Due more to paranoia than anything esle, he lives off the grid. Cut to T3. Now we don't have the messyness of Cyberdine having been blown up already, no T1000 to deal with, etc. The way you explain the events of T3 is that Arnold plays hs role from T2, but the TX isn't here so much to kill John, but to insure that Judgment day happens. Messing with the timeline back in 1984 has caused ripples that could ultimately destroy the Skynet ruled future. So, in another paradox, the latest Terminator prototype is sent back in time to ensure that Judgment day does happen and the time ripple anamoly doesn't cause them to never be created. John has the chance to stop all this from happening, i.e. "no fate but what you make," but blows it. The movie would be a total downer. Plus, it would give more depth to John's character because he wouldn't only be the hero of the human resistance, he would also be part of the reason there had to be one.
The third movie could go about the war between man and the machines. It would be awesome to finally have a movie set in that time period. It would be set at around the end of the war, and at the end of the movie, just as victory is won, a terminator is sent back in time to kill John as a boy. John has no choice but to send someone back to protect himself, and hopes that perhaps this time he could even stop this hellish future from happening. T2 becomes the fourth movie and the end of the series.
There would have to be a lot of little edits, mostly in T3, but it could happen and whoa...I am really liking this idea. If they do come out a fourth Terminator movie, and it set in the future like they are talking about, then changing the story to this might even be possible. Oh man, would that be cool....