Don't put too much thought into that.

Chances are it was an oversight on the MK Team's part.

You're right. Most of us noticed this when the game came out.

The question is why, since Raiden never really changed his path, so he would have done everything the same in the old timeline but had no personality there until malfunctioning between MK4 and Deadly Alliance.

That was possibly the biggest blunder of the Grandmaster in case it's true seeing Sektor kills him in his ending. Maybe the privilege was directed for the loyal leaders.

If I'm not mistaken, the "emotionless" personality of Sektor was just a gag used in MK: Deception's Konquest Mode to portray a bug, working error, etc. And in MK Gold and Tournament Edition we never saw how Sektor behaved with other characters... I mean, he tried to kill Sonya,Jax and Cyrax, be he didn't spoke.

My personal thought on this matter is that the Lin Kuei technologies are NOT irreversible in spite of Grand Masters beliefs, and in MK: Armageddon he clearly shows signs of rage and adversity towards Taven.

Retcon or not, I think its an improvement.

I always liked how Sektor, in essence, was just corrupted programming, and whoever he was before the automation was basically irrelevant. I guess I don't mind the current Sektor, but he doesn't seem as interesting to me. He doesn't have much of a personality beyond just being a douche.

Maybe it's an example of the butterfly effect; Raiden changed Cyrax's path, leading to him to being more vocal about his disdain for automation, and even making him try to leave the Lin Kuei outright and disobey Sektor's orders. Sektor could've been allowed to retain more of his autonomy after bringing Cyrax back into the fold, perhaps proving that his own loyalty is unquestionable and that he wouldn't need a "slave" drive to do what was best for the clan.

Yeah like what everyone said, Sektor wanted to do the Cyber Initiative and he is fiercely loyal to the Lin Kuei so they didn't make him into a mindless machine. Fail on the Grandmaster's part.

This.

Isn't Sektor also the Grandmaster's son. I mean wouldn't that fact alone entitle him to some special treatment above the others.

This and the fact that he is fiercely loyal to the Lin Kuei, the Grandmaster probably thought he didn't have to worry about his son betraying him. He's completely wrong but still.

Considering that the Grandmaster automated his own family leads me to believe he doesn't care much for him. I doubt he would have given Sektor less rigorous programming.