Eh. If violations of physics and common sense (never mind unusual cognitive-science concepts) in space opera had the ability to make me angry, I'd have to spend most of my time getting angry. Mass Effect actually seems fairly sane as space opera goes, though its handling of the robot rebellion motif is pretty damned ham-fisted.

The most recent Deus Ex game actually bothered me more, thanks to explicitly tackling transhumanist themes and then completely failing to resolve them in a way that showed any understanding of the subject matter. Very little in media irritates me more than a work rendering complex philosophical issues down into a trite moral quandary and then trying to award itself cool points for knowing about the issue at all.