I for sure don't miss them working together :)
Anyway, i didn't see Raph as mean-spirited. More like tragic. He's lost. He's angry that he's lost. I likes his arc very much.
Not sure what unsettled you about Dean though. His attitude and his words about missing fathers gave Cas sp needed hope. And he clearly wasn't happy to be alone - watch the scene again. He can be partly right about not having sam around because sam (esp right now) is dead weight that drowning Dean but be alone? It's Dean's mask again. Bravado. Nothing else.