It was extremely obvious that the Scavs were human and Tom was doing the alie...sorry Glados' dirty work from early on, however the cloning thing got me good, even though it was hinted with the 'radioactive' no-go zones.
From the moment you see the 2nd Jack has escaped when he comes back down the surface, you knew he'd pop up later in the movie, and the moment you know Jack switched the passengers at the end, you saw the happy ending coming, but that was kind of acceptable given the fact the human race nearly got wiped out. The idea of the self thing was given such a brief going over in the house by the lake scene, it felt like it deserved more exploration, especially given said ending and Olga seemed to be pretty cool dealing with a mind-bending scenario.
The biggest thing that bugged me though was the ending - it just seemed like lazy writing after all that- I was hoping for more than a dumb computer with a red eye:
Glados - wait a sec, you're up to something, can't be anything like when those pesky humans stuck a fuel cell in one of my reactors and blew it up, can it?
Jack - no lol
Glados - oh right, come on in... btw I can monitor you physically from a distance but I'm ignorant you're carrying a dude in the pod not a lady... now come stand right in front of me so I can babble
Jack - oh hai, I brought a big bomb!
Glados - oh noes! Send the drones, but don't fire as soon as you have a visual, wait until you're within an arm's length
Jack - kaboom!
Sigh.
Also, and this is a proper nerd criticism. I'm sick of the idea that aliens would need a planet's resources - you have clouds of water in space bigger than gas giants, belts of rocks with all kinda of elements in, why the deuce can you travel the stars yet not use any of that and instead go to extreme lengths to harvest a tiny speck of rock and water? And for what? It seems a bit crap to need all this energy when you're essentially a giant waste of space robot that's mostly empty space, that doesn't do much except float about. Can't we have something more thought-out than 'need energy, kill all humans via energy-inefficient means'?