Yeah, that's always been my problem with Mass Effect, and a lot of other games and movies. The 'hero' is a roaring neanderthal, while the 'villain', while definitely a bag of dicks, has reasons why they do what they do. Saren and Illusive Man, while being horrible people, explain why they do what they do, and I can at least nod and understand how they came to do this, which is more then Shepherd ever did. Shep never has a single moment of weakness, not a single attempt to consider the enemies position or doubt her own conviction, she just stomps and yells and repeats the same bland black and white moral outrage whenever faced with anything grey.
It's not a deal breaker for me, but it's been a constant irritation. I don't expect Shep to come to Illusive Mans side, but a few seconds of independent thought would be appreciated. Hell, the only time I remember her ever having a moment of weakness, it wasn't about whether or not Cerberus or Sarens alliance are necessary evils in a very real extinction event, it's whether or not she can round up a big enough posse.
Basically, Shep is a thug to me.