Yeah, I noticed the different look for D'Argo too. I think they adjusted his coloration somewhat.
To me, Scorpius is always an interesting villain. You never really know what he's up to, or where he gonna go. He has more facets than most villains.
The thing in his head is
It's explained a little later in season 2.
My favorite episode of season 2 (maybe of all time) is Out Of Their Minds
. I won't spoil it for you, but it's a crazy one.