The moral choice system in Infamous pissed me off too. Because it wasn't a choice. I enjoyed running around the city killing civilians. If I wanted my skill tree to actually extend to the best powers, I had to either cut that shit out or be a dick, I went with the second option. Not because I really wanted to, I actually was kinda tempted to be a good guy occasionally, but because the game was all but forcing me to choose one.
Hell, a mate of mine accidentally picked a major evil choice after a mostly good playthrough, which totally screwed him over since it shot him from mostly good to almost entirely evil, which negated most of his upgrades. It's a poor system, which is a pity, cause I'm with Yahtzee on it being the only major flaw. Haven't played Infamous 2 yet, probably won't until I get a PS3.