This was a prime example in my opinion of too much going on. The fact that 3 characters died meant that time dedicated to each one could never be distributed evenly. In many respects I'm glad they used the majority of the time to focus on Rufus, as he was truly one of the better characters belonging to the series. His interactions with Bobby were some of the most heart-felt, although I'd have liked to know more about this supposed Omaha incident. It sounds like the kind of thing that they could have used in a future episode. I suppose we will most likely never know now, unless we get another fantastic Bobby Singer monologue.
I was disappointed at Mitch Pelligi's departure as well. His character was never fleshed out enough, it felt linear as he never looked bothered about killing his grandchildren for his daughter. Imagine telling her he'd killed her children to get her, I'm sure she would not have been best pleased. With regards to Mitch though, he is truly a fantastic actor and it's a real shame that they couldn't work him into the storyline better then some of the episodes he was in.
The story itself was a bit lacking really, the whole The Thing/X-Files element was obvious and although it was never obvious who was infected, when someone goes to the toilet on his own, the chances of him being infected are pretty high.
A good episode, a bit lacking in story. The scenes between Bobby and Rufus eclipsed anything else in the episode, and the climax was emotionally charged with the death of Rufus. Since watching it, I've felt that there wasn't really a need to kill off Rufus; A fan favourite that could contribute with great acting and humour. Here's hoping that he's not actually dead, and that they were referring to Samuel by using Rufus' name....You never know with Supernatural right!