Off the top of my head, one of the earlier screen shots for Fall of Cybertron featured Cliffjumper, using Bumblebee's body, but Prime Cliffjumper's head, and the concept art for what is presumed to be the Nemesis in FOC looks exactly the same as the Prime Nemesis design.
Look at his head! LOOK AT HIS HEAD:
http://www.tfw2005.com/transformers-...1318472757.jpg
Meanwhile, the Prime tv show has taken some basic visual elements from the WFC video game to represent Cybertron and Primus (or as the game vaguely refers to him, as the "Core of Cybertron"), with the backstory based upon Hasbro's own story bible for the Aligned continuity (Dark Energon, corruption of the planet's core, the bestowing of the Matrix of Leadership onto Optimus).
It doesn't really matter what High Moon thinks or what G1 references they have inserted into WFC/FOC. They're marketing their game towards a gaming audience who vaguely know Transformers, and quite frankly, there's not that many G1 references in WFC anyway that can't simply be repurposed to be something that also happened in the Aligned continuity. No, I do not count lines cribbed from Transformers The Movie as continuity reference.
This is what the wiki refers to as a Continuity Family. You know how the G1 Marvel Comics, the G1 Cartoon and various other G1 continuities can in no way work together, yet are still considered to be G1? Same thing. Aligned (the Prime universe) is a Continuity Family, under which many different continuities, often with some commonality but otherwise might be difficult to reconcile with each other, can exist under one umbrella.
I don't know why people are so offended by the notion of WFC/FOC being part of Prime.