The choppyness only really kicks in during the final act (and that's pretty much explained by the production background story).

It may be that some of the Kyle /Marcus material that was scripted was also filmed and might turn up in some extended version but that wasn't edited in a detectable choppy way (at least going by my one viewing of it) the really problem is that final reel.

We now don't know why Skynet has a human styled control centre or why they are kidnapping people and loading them into brain scanners, which is something that could have been scripted around without having the Project Angel stuff. It could be explained as Skynet wanting to make more units like Marcus, heaven's knows he would be able to sneek into human camps better than someone like Arnie, a Terminator shaped after the old lady or the mute girl would be even less noticable.

Hopefully an extended cut and/or deleted material will make it onto a future DVD release and we can get an spoilt star/internet fanboy panic free version that takes it beyond being the good movie it is into the really good movie it should have been.