I'm sorry, but there's no getting around it--this episode opens with Ian just straight up murdering someone's pet by bashing it with a rock until it falls into a bottomless pit. I have no idea how the RSPCA didn't step in here. I just bet that in between each and every one of his scenes, the Black Dalek went back to his room and just sobbed openly, fondling the Slyther's collar with his sucker and whispering, "Why? Why?"
Okay, maybe not so much so, but it's still interesting to me that this is an era where the Daleks haven't fully ossified as a concept. They're capable of having pets; they view other life-forms as insignificant and not worthy of notice, rather than as targets to be exterminated. They enslave rather than kill for the most part, and even feel outrage at attacks against them (it's surprisingly funny when one of them talks about the "unprovoked attack on our saucer"). They're conquerors, but they're conquerors with a purpose rather than genocidal maniacs. It's a smaller difference between the Daleks then and the Daleks now than it was in their previous appearance, but it's still noticeable. They're still characters and not monsters. That won't last much longer, so enjoy it while it lasts.
The role of "monster" in this story is taken up by the Robomen, as Larry's search for his brother ends the only way it really can in a story like this. It's still a pretty good scene despite the obviousness of the trope, as Larry begs Phil to remember his wife and family and is shot in the gut for his troubles. None of it is surprising--it's all exactly what you would expect, right down to Phil whispering Larry's name as he too dies--but it's still hard to look away as it's happening. The Robomen really are such a good part of this story that it's amazing how rarely they've been used since--they really are more effective at being Cybermen than Cybermen are in some ways, both because they have this wonderfully horrifying air of neglect and despair, and because of the utterly horrific descriptions of their eventual demise ("they go mad, bash their heads against walls...") They're the dehumanization of oppressed people made brutally literal.
Of course, there's also the other kind of dehumanization that happens to oppressed people on display here. Barbara and Jenny's run-in with the collaborators is far more affecting than the Aaru version (what, you think I was going to get through all six episodes without referencing the Aaru version?) precisely because they never get their comeuppance; in the movie, they die the kind of gruesome death that all traitors deserve, but in this version they're out-and-out rewarded for their treachery and deceit. It's the kind of lesson Doctor Who doesn't always teach...sometimes, the bad guys get away with it.
As with the rest of this story, though, the weak point of "The Waking Ally" remains the star and main character. (And presumably the titular waking ally.) Their segment of the episode is nothing more than a slow trip to join the rest of the cast in Bedfordshire, and even the fact that Susan finally gets something useful to do one whole episode before she leaves the series for good doesn't change the fact that all they get is a boring fight scene and a bit of "science-y" exposition that again sounds like the Doctor is suffering from mild aphasia instead of a technical explanation. Again, it's hard not to feel like Nation doesn't feel like he has to try now that the Doctor is firmly cemented as The Hero; he was much more interesting when Nation saw him as a force for chaos rather than writing him as an agent of order.
But at least we're headed for a climax, right? Ian's hiding in a nuclear bomb, Barbara is infiltrating the Dalek headquarters, and the Doctor and Susan...are somewhere in the general vicinity. Better late than never, Doctor!