I feel exactly the same way about this season. It's the season that brings us Riley (dull), Adam (kind of silly), and Where the Wild Things Are (the badness is self-evident). But, as you point out, there are just so many fantastic, high quality episodes (off the top of my head, I'd add Who Are You, New Moon Rising, and The Yoko Factor to your list -- and I have an odd affection for A New Man); we get the return of Spike, in great form, and we get Tara. All in all, the good far outweighs the bad for me. I don't quite get why people don't like this season.
I also agree about The Initiative -- not an episode that I'd rank with the others, but still really good, with one of my all-time favorite scenes in it. I actually tried to sign up to co-host this episode just to talk about that scene, but you got there first! I'm very excited to hearing your and Bryan's thoughts about it.
I agree about A New Man, and I also liked This Year's Girl, The Harsh Light Of Day, and Doomed (loved Spike's speech - "Come on! Vampires! Grrr! Nasty! Let's annihilate them. For justice - and for - the safety of puppies - and Christmas, right? Let's fight that evil! - Let's kill something! Oh, come on!"
And yes, both Lindsay Crouse and Seth Green left earlier than planned. and the season suffered for it. The Veruca storyliine was supposed to go on for quite a while and was compressed into one episode.