Finished this fantastic game... and I can't believe how much I missed! (SPOILERS)

[WAU]

Let me see if I have some answers for you...

• Who built the body Simon is in and why? Who activated him and why? I know that the body is Imogen Reed's but other than that I'm stumped...
  The WAU did. The WAU, trying to preserve humanity, started uploading human minds into robots, to try to populate the world with new 'humans'. However, these robots always went insane (e.g. the monsters you see, Carl Semken, the K8, the DUNBAT...). Somewhere in I think the Climber Catherine comments to Simon that the reason these robots went insane was that they were humans stuck in non-human bodies. Simon the WAU's newest take on that: 'a sound mind in a sound (i.e. human) body'. In other words, Simon was the WAU's next experiment, and the WAU was 'hoping' (and rightfully so) that this new human-robot hybrid wouldn't go insane like the other robots.
  
• Why did some people get "stuck" in the robots? Why did others get turned into monsters and still others were put into the structure gel? Is it all the WAU's doing?
  No one got 'stuck', they just had their scans uploaded into those robots and they don't know about it. Carl Semken makes this especially clear: he was unwittingly scanned by the WAU while operating a remote robot, and since he doesn't know he was scanned, Robo-Carl doesn't know he's a robot. I presume that the monsters (which are just plain robots) have a similar story, except maybe they were earlier prototypes by the WAU, which caused them to be more insane.
  
  The structure gel can only attempt to preserve existing human bodies, i.e. real humans. That's not enough to populate a planet, so the WAU started copying brain scans into robots, simply because then the world would have more 'humans' around.
  
• How do you know the names of all those monsters? I can't remember them being named in-game.
  Good question. I know that at least the face-rapey tentacle guy in Tau could be inferred to be a guy whose name I forgot from a terminal in Tau, but as for the others I wouldn't know.
  
• How do you know one of them is Akers? I read about him a lot, but... huh?
  I had the same question: we know that Akers is an eyeless monster (because we find his eyeballs lying around at Delta), and we do find a lot of those monsters in Theta, but I never figured out if one of those proxies is definitively Akers.
  
• How do you know the guy from the last part is Johan Ross? I don't even remember that name, although I probably read it somewhere.
  A logfile at I think Theta talked about Johan Ross having died and being brought back to life by the WAU. We also learn from a blackbox near Tau that he's the AI psychologist, and from another blackbox just past Tau that he's supposed to be the only one who knows where Alpha is. Additionally, the guy that keeps stalking you eventually helps you unlock the Johan Ross room inside Tau, and this guy also wants the WAU destroyed because it's supposedly out of control. All of this points into the direction that this guy is, in fact, Johan Ross.
  
• What does Johan Ross actually want? For you to kill the WAU, yes. But why?
  He once says: 'can't let the WAU continue producing its filth'. He believes that the WAU has gone out of control in its quest to preserve humanity, and that it's only causing more suffering (e.g. the insane monsters). He believes that the WAU will never be able to recreate a proper human being (and even if it were, would that human being really be 'human'?) and as such it should be eliminated to prevent more misconstructed insane robots.
  
• When do you learn that all the beheaded bodies are due to the WAU detonating the black boxes? I read that on the forum, but I didn't even know those things were in their heads.
  I think you can find a blackbox instruction manual somewhere in the Theta labs, and I believe a radio transmission near Tau explains that the WAU blew them all up when Ross talked to Herber about destroying the WAU.
  

Oh, and by the way: Am I the only one who didn't kill the WAU? I never saw someone mention that here. I didn't do it and it didn't seem to impact the game at all.

I didn't kill it either, because I fundamentally disagreed with Ross (Simon and Catherine seemed pretty okay humans to me, and with Simon being the latest iteration it seemed clear to me that the WAU was getting better at creating proper human robots; I believed that in the end, more Simons and Catherines and so forth would be able to work together with the WAU to create more brain scans (e.g. merge two scans to create a new person?) and to eventually create more humans, saving the species... in a way).

I have a question of my own, though...
Johan Ross is an ordinary human with some robot parts slapped on to replace human organs that were irreparably damaged when he died, right? If so, how could he have climbed down with us on the Climber without being crushed like a can of soup, when our own Simon in Imogen's body would have died? You could argue that the robot bits are strong enough to survive the pressure (so Imogen's body would be crushed leaving only Simon's cortex chip intact, which is obviously bad), but this doesn't explain how Ross's brain, face, etc didn't undergo precisely this fate as well.