Well, Dyson said the microchip and arm took them in directions they "would never have" thought of (although, for all he knew, they might have).
However, that wouldn't have been neccessary. Once the basics of whatever T1-era Skynet had as a foundation, were thought up, it was then inevitable. A case could easily be made that if Skynet had arisen from the events of T2, it would have been more powerful than it initially had been.
Back to the new film (because this thread will have to be merged with the other one, otherwise), I really don't see it having the same effect as 'Genisys'. An awful lot of fans and, more importantly, casual viewers, tend to dismiss the third and fourth 'Alien' films. If this film does negate them, all it has to do is to be at least equal to them in entertainment terms (being more so would be an unquestionable bonus). Nobody's said it's going to wipe the first and second out of continuity.