I enjoyed Lifesigns. But the Doctor is one of my favorite characters. Shmulus will be back in the future!
The B plots were well, part of the ongoing subplots in season 2. Jonas is playing spy with Seska and Paris is being a total screw up. Even as he's doing this he does go out of his way to help out the Doc though, which is almost contradictory to the rest of his behavior of late.
They will come to a conclusion in the near future... won't say any more until you get there.