All three games in the trilogy have a different atmosphere and overall feel: in the first it feels as though a great mystery is unraveling as you progress, and everything is just a little more alien. The second game has more of a nihilistic, impending doom kind of feel to it. The third is of course all-out war and desperation, and the smorgasbord of emotion that comes with it. The question which I ask you all is which one is the best and why?
Personally my favourite is that of the first game - I don't know if it's the soundtrack, plot turns, unusual level design or general aesthetic, but everything feels quietly unsettling. Like you are constantly on the verge of something. Plus when you're exploring an uncharted world or derelict ship, you really do feel alone. Brightly lit and silent is far more unnerving than dark and noisy in my opinion.