Via press release:
Smith will play a new character with a strong connection to John Connor, alongside Arnold Schwarzenegger, Jason Clarke, Emilia Clarke, Jai Courtney, J.K. Simmons, Dayo Okeniyi and Byung Hun Lee.Well, that would be the easiest possibly way to explain why John Connor's timeline keeps changing. Especially since this new trilogy is, from what I've heard, pulling a kind of Back to the Future II routine on the original movies (though it may also do like the Sarah Connor show and selectively ignore the two sequels most people dislike).
We're also conditioned to believe that Matt Smith doesn't have too tough a time defeating evil cyborgs. In fact, once this movie is behind him, he'll be an "Ex-terminator" star.