I really hope O6 is wrong about that. I really do. The over-use of Primus and Unicron is one of the worst things to happen to the franchise. (In some ways, I dislike them more than I dislike even Skids and Mudflap.)
Damn this country for getting more superstitious in the 90s. Damn the "X-Files". Damn cringing peasants who persist into the 21st Century. Damn childish tendencies towards "magic" in our culture.
(Okay, sorry about that. I blame evil spirits.)
Which again I say isn't accurate. Like I said, it is clear the Oracle/Vector Sigma have access to the Allspark/Matrix/Primus, but they are still established to be something separate, and although Primus can in-turn control them, they are not a manifestation/aspect of Primus himself.
I tend to think that the original intent with the Oracle, (and retroactively Vector Sigma), was the Greek model you describe. But, the idea was later retconned in during "Universe" and the UT.
Doesn't matter what kind of reprogramming, if it reprogrammed him to affect his decisions in the slightest, it is still guilty of taking away his free will to some degree. And again, I can't see the Oracle doing this when free will is to be one of the themes of the show.
The subversion of free-will was also a theme in "Beast Machines" though. And, nobody (at any point in the franchise) ever accussed Primus/Oracle/whatever of being over concerned with the well-being of TFs as moral ends unto themselves. If the Oracle is going to be operationally fine with Megatron committing genocide and effectively destroying millions of years of TF civilization, would it really be squeamish about "nudging" one 'bot in the "right" direction?
It's a case of rigamarole and constant retconning. People were pissy that the Oracle messed up their "perfect" mechanical Cybertron, so 3H said that those goofy aliens were controlling it the whole time. And nobody liked *that* explanation because it's 'stupid' so the new club retconned *that.*
Post-hoc fixes are a common problem. (And, failure to learn from the past is becoming more common as well.)
Sipher and Troop took the 4th part of what would have been an aimless and endless story and brought it to a resolution. Yeah, they undid the stupid "fix" Hallit came up with to pander to fans who did not like "Beast Machines". That was likely as much a shot at Hallit as it was a "fix". But, it brought things to as clean an ending as they could have been.
But, I see, and agree with, Sparky's general point. (Never thought I would say that. At this moment, Sparky's very soul is being re-written to "fix" this problem and restore balance.) Hallit had a "no, this is what really happened" reveal, then Sipher and Troop followed it with a "no actually, this is what it really was" reveal that just served to convolute the whole damned thing even more.
Both were, ultimately, changes for the sake of pandering. This is as self-indulgent as writers deciding to "change" a long-standing status-quo just for the hell of it. The return of Jim Hammond during Byrne's run on "Avengers" is another example of this. (I have tremendous respect for Byrne and the Marvel of that time, but I have never thought this story was a good idea.) Somebody, (likely Byrne, maybe Thomas), wanted to bring back Jim Hammond while keeping the Vision in place...and we got a stupidly back-written explanation that served no purpose beyond bring back Jim Hammond and reading like a bad fanfic.
Then, years later, somebody (Busiek I think), decided to "fix the fix"....and wrote an even worse fan-fic, (only it was official!), story revealing that both the stupid Byrne reboot and the thing it undid were correct.
Dixon is guilty of this with the Stephanie Brown/Spoiler fix.
Dom
-of course, better writing and editing in the first place would remove much of the temptation to "fix" things.