In the third season finale titled Resurrection it is implied that Sydney is essentially Jack's pet project - most likely concerning Rambaldi and his prophecies. When she is reading all the secret files about her life, her father enters the room and says: "You were never meant to find those." Later it was very akwardly retconned so that the files only stated that Jack murdered Irina. Stupid move since it would have made much sense if Jack would have been revealed to be the man behind The Covenant and a far better follower of The Order than Arvin Sloane ever was. Also I can't imagine a better nemesis for Sydney than her own father. Was the fourth season a pinnacle of network interference or just a really dumb move by Abrams and the writers?
There was a similar TV/M thread on this back in January that I don't think it'd be too late to add to.
Yes, I posted in that thread, but it didn't really take. In my opinion Jack as a bad guy had tons of potential and it could have totally changed the dynamic of the show. I can easily imagine that Sloane's redemption could have been very real and he could have turned out to be a good surrogate father of sorts for Sydney - despite their troubled past to say the least. Also I'm guessing that it was Jack who stabbed Vaughn in the back. There was really no reason to hide the identity of the attacker from us if it truly was Katya Derevko like Vaughn suspected later on.
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.
IIRC season 4 had a different showrunner than season three did. The new guy probably decided to go in a different direction (and I'm assuming with some new marching orders from ABC) since he would have his own ideas about the show he would want to use those rather than someone else's.