The concluding chapters seemed rather anti-climatic.
I'd agree with you about the very last chapter, Parson, but for me the chapters dealing with Rex and the assault on the facility were very necessary to end his story. I can see why that very last chapter is there, because it could be argued the novel isn't about Rex at all, but about the wider battle in which Humos is the protagonist -- that's certainly Humos's view, of course. As I mentioned above, I didn't like its chapters (nor the other intervening ones at the end with the extracts from Maria Hellene's book), but again I can see they're there to give the wider picture.
Why Rex's team thought so highly of him at first is baffling.
I don't know that they did. Dragon is openly contemptuous of everyone else, Bees doesn't seem to think on an emotional level, at the beginning at least, and Honey seems to treat him as someone she's fond of, but who is nowhere near her intellectual equal, much like we might treat a clumsy child who is a distant relation, or an old friend who is decent and honourable, but is a friend simply because you've been through so much together. However, the others are all bound by the hierarchy system that's an integral part of their programming -- they have to obey Rex because he's higher up the chain of command. At one point Honey says something to the effect that she will tell him what she's doing/thinking if he orders it, but she would prefer him not to ask, and because he recognises that she is more intelligent than he is, he doesn't ask. Plus his orders are correct for the situations they're in and in accordance with their training/programming, albeit Honey manipulates him when she can so those orders are more humane/palatable to us, so there's no reason for them not to go along with his wishes. But to my mind that doesn't equate to thinking highly of him.
I would have liked the story to have focused on Honey or Bees, much more than Rex.
I don't think I could have coped with Bees! As the least human of them, she/they would have made things very difficult to follow -- I had problems enough understanding her communications! And Honey, I think, would have made less of a story, in that she doesn't grow in the way Rex does. She learns more of what is going on, so confirming her suspicions, but she doesn't develop -- she's intelligent and manipulative at the beginning, and is intelligent and manipulative at the end. So as a protagonist, she'd have no character arc to speak of. Plus she knows more of what is going on so the Humos mystery would be over and done with far sooner, unless she was also withholding information, and too much of that can be very annoying in a story.
There always seems to be a key player off stage that is never truly revealed, only hinted at.
That "always seems to be" is, I think, a real understatement! There's definitely a key player manipulating everyone, but although the early chapters are cryptic, I thought Humos was pretty much revealed by the end, even if we can't be sure exactly what form it takes. I don't like that kind of puppet-master stuff, so actually I'd have been happier without his appearance and just left with nothing more than hints of something going on in the background.
But I'm glad you think it's worth recommending, even if you didn't like all of it.