There's a pretty dramatic shift in the writing between seasons 3 and 4, which I think has a lot to do with the re-writing of the cliffhanger. Season 4 is, in my opinion, the worst season of the show. They tried to do a soft re-set of the series by introducing APO (which put Sloane back in charge... which made no sense to me... but whatever) and showcasing Sydney and Nadia as the kick-ass super spy sisters. The on-going story arcs and big cliffhanger endings disappeared. There didn't seem to be any cohesive arc to season 4, just random stand-alone episodes, until much later in the season, and what they came up with was quite convoluted.... even more so than usual for this series.
I think it was all network tampering by ABC. They kept meddling with the creative direction of the series because they thought it was too smart, too complicated, and not friendly to new and casual viewers. It was the network that demanded the writers end the SD-6 double agent plot early, and I suspect it was also ABC that wanted stand-alone stories and simple plots. More action, less substance. I'm pretty sure that the writers knew where they wanted to go with season 4, then ABC probably stepped in and mandated creative changes. The network may have even vetoed the idea of Jack turning into the villian, if they didn't like the idea, hence the retconned season 3 cliffhanger.