Twi'lek sideboob indeed.
Well played sir. I hate to admit, but I am becoming a little fanboyish for Shamus...
I agree that spy stories need conspiracies (what would be the point otherwise?), but I think it's pretty clear that the plot in AP has holes where cut content was supposed to go.
Just take the overall premise: . That's dumb and obviously should have been an eventual discovery as you go through the missions.
I didn't really have a hard time keeping track of the characters' motivations (as in the ones they'd actually told you about), but because of how the game is structured a lot of the time Mike will know stuff you haven't been told when he's talking to certain characters. Him talking to Albatross is the easiest example (he says "You again" even if you've never talked to him).