Interesting ... a few of the episodes you listed as strong ones, like "Barge of the Dead" and "Someone to Watch Over Me," are among my least favorite. However, I do agree that "Tinker, Tenor, Doctor, Spy" is a good one.
Maybe it is just that I happened to run into a stretch of episodes I liked, rather than any particular change that took place mid-season.
"I don't mind the fact that race, creed, sex, ethnicity, and the disabled are protected classes, but I draw the line at stupidity." -- Jethro Elvis
: Attack otters of the ass. In submarines.