Totally agree with the things other have said about seeing more of the Nova Prime history, and his slow change of ideals.
I love that the Annuals have been used to do some pretty major world building, in terms of Transformer history, and setting up some other players within the universe.
I see at as two ways of telling the same story, with different focuses, and therefore a different choice on what to emphasize and what to leave out. One story set in the physical reality, and the other in the more metaphysical space.