ok, so to summarize:
Phoenix is the primal force of creation
Unicron is the primal force of destruction
Phoenix was able to overcome Marvel's primal force of destruction (M'Kraan Crystal)
Unicron was able to overcome...umm...Hasbro/Marvel's primal force of creation (Primus).
So in both cases, they've overcome their polar opposite. That about right?
They're all-powerful forces who have been described inconsistently over the years and seem to conflict with other canon in their respective universes, like the role of Primacron in the Transformers comics or the role of LT in Marvel.
Sounds like a stalemate to me. Or at the very least, inconclusive since they've both gone unopposed and unbeaten. Minor edge to Unicron since he seems a bit more unstoppable. But that may be just because I know less about him.