There are many choices I agree with here, especially Anders in DA2.
The one that annoys me the most, however, is Legion in ME3. In ME2 it made perfectly clear that the difference between the geth and the heretics was that the heretics accepted the reapers' future while the geth wanted to build their own, even going so far as to acknowledging that Shepard is more similar to them than it had thought if Shepard destroys the collector base. Yet in ME3 they suddenly go with the reaper upgrades anyway. Okay, their collective intelligence was decreased and they fought for survival, but to just turn on such a fundamental ideal felt off.
Also, the whole individuality thing. The geth are perfectly happy with being a collective intelligence, that is their preferred way of existence. This is even acknowledged in ME3 with the sphere they were building around their star to house all geth so that all geth could be together and be entirely connected in one huge collective consciousness. But when they get their reaper upgrades they suddenly go all "Wee, individuality, hooray, now we're really alive". They already were alive. That they were totally different from humans did not make them less alive.
I still really like ME3, but things like this make it very difficult to do so sometimes.