Overall, I really like this game (the Thorton, Inc. ending, in particular, is just sheer undiluted badass, especially killing Leland with the "data disc"), but I do have a handful of quibbles that stick with me.
1. In the Thorton, Inc. ending, if you leave Leland alive, Thorton is still implied to have taken over Halbech. But...how? If you don't kill Leland, he's still the CEO. (Or the CTO. Or the Chairman of the Board. The game seems to get a little fuzzy on this point, but he's definitely the man in charge.) And there's no way Thorton can implicate Leland in Alpha Protocol's crimes without also damaging Halbech, perhaps irretrievably. So how can Thorton take the company over if he didn't do away with the guy already running it?
2. The Halbech missile data in Brayko's mansion, which is apparently so important that it's considered to be a reasonable option to abandon SIE/Albatross to be tortured to death to get it. I've done the mission both ways (first skipping the intel to go after my handler, then using my Technical Aptitude to be able to get both), and I don't notice any difference in the subsequent missions. If this data is so important, why is it never mentioned again? Or is it mentioned, and I just missed it.
3. In Taipei, Omen Deng works for President Sung. And the evidence you showed Sung about the assassination or the riots came from a hard drive you stole from Deng's men, with the implication being that Sung is completely in the dark about both issues until you tell him. So...why couldn't Deng have gotten a message to him (they have to have some way to communicate, or Deng's status as a deep cover agent would be useless to Sung) and warned him about both plots?