I never really bought how unquestioningly accepting almost every human character outside of the Terminus Systems is of the Alliance from the second game onwards. You'd think a huge supranational government wouldn't be all sunshine and rainbows.
I feel like the idea of Alliance being more morally grey was kind of canned after the first game. Missions like The Negotiation and Espionage Probe are favourites of mine because they expose some skeletons in the Alliance closet. Is this political bias on the part of BioWare or am I reading too much into this?