The one story framework was meant for both WFC and Prime to be drawn from, or at least inspired by. Since both ended up being developed independently, they both veered off in different directions with distinct similarities and some similar items that had different properties (like Dark Energon). Just like the original Gen1 comic and cartoon being inspired by the original Gen1 Bible, both veered off in inconsolably different directions, but maintained similarities.

Since storylines of both WFC and Prime have progressed significantly now, it would be difficult to reconcile them without it feeling really cheap or just really awkward... a bit like trying to shoehorn any series into a previous one or Gen1 itself.
I think it is best to see both WFC and Prime as alternate realities of the original concept that Hasbro had developed for both companies to use... and then decide which one did the better job at interpreting and telling that story.