I wouldn't say that fans forget, at least not completely. For more than once someone has asserted that Sunbow-Mindwipe must have been a Unicron cultist, per his line re: "the powers of darkness", only to be reminded that it isn't necessarily so, as a strict reading of Sunbow continuity would make Unicron the Dark God of Precisely Nothing.
But Furman does cast a long shadow on Transformers writing. Rather than complain, though, I view it as his having had the time, in a slower medium than an 86-minute feature film, to craft the story with a little more care that might have been warranted for toy-based storytelling. (Certainly he's marvelled at how much reverence we've had for material he never expected to last....)
In TF:TM, as you say, Unicron just shows up with no explanation, and has a very specific weakness. We never learn why a talisman in Autobot possession is "the one thing -- the only thing" that destroys him, and the movie moves along at too fast a pace for anyone to pose the question.
So, in the early 1990s, along comes Furman with the Matrix Quest. It retcons two things at once -- merging the object we know as the "Matrix of Leadership" with Budiansky's "Creation Matrix" (originally an intangible program), and giving it a reason to harm Unicron (the Matrix filled an Ancient Death God with life -- so he blew up). Along the way it explains why the bearers of the Matrix take the second name "Prime".
It's very Manichean. But it works, and gives the extant prior lore a bit more depth, in terms of "Oh! turns out the Deus ex Machina ending was really a Machina ex Deo, and in the manual* all along!"
*(By "manual", of course, one means the Covenant. But that's another story....)
