Enslaved was an interesting example of how overlooking sympathetic characters can disrupt emotional investment with them. You play Monkey, a guy that escapes from a robotic human-harvesting ship with a mechanically inclined woman named Trip. Trip is distrustful but needs your help so while you are unconscious, she slips a device on you that will kill you if she is killed, forcing you to stay with and protect her -- a device that later begins messing with your mind.
Monkey is pretty sympathetic in this situation. He barely escaped alive and seems to be a pretty free-roaming character trying to make his way through life, and with pretty good skills. Trip pulls a pretty dick move with the "enslaving" device, but they play it pretty cautiously and she remains just sympathetic enough because she's clearly afraid and less experienced, and it's enough that the writers have room to build a real relationship with them. In fact, I found their rebound from this action believable enough, and I liked seeing the two characters draw closer.
Unfortunately, throughout the game, Trip never sees a reason to actually remove the collar, and this fact not only gets in the way of the building relationship, but Trip decides at one point, about halfway through the game -- after Monkey has given her more than enough reason to trust her -- she effectively says, "Sorry: I know I said I would remove the device after x happens and that you would help me even without the collar; buuut I'm going to keep it on effectively force you to do something else, and void any premise of a relationship we've built between us." I had to mentally block this moment from the story to even enjoy anything that had to do with her from that point forward.
This is a serious breach by Trip, but another character -- Pigsy -- appears that could give emotional attachment a chance to rebound. First impressions are a bit shaky: Pigsy is a fat, dirty, competitive hermit that is reluctant to help, and that wants to sleep with Trip doesn't really help. At this point, you might be able to call him so pathetic that he's sympathetic, but then they have him basically attempt to murder you to get you out of the picture, and suddenly I'm traveling with two horrible companions that have no qualms with murdering me at the drop of a hat.
Enslaved felt like a pretty rushed game so my inclination was to forgive the developers of mechanical problems, but the story seemed very much under their control, and worth critiquing. I never could build an emotional attachment with these characters. Or rather, when I did, it was always betrayed by them, to the point where it was hard to care what might happen to them. I realize some of it might be related to the Chinese legend the game is based on -- I don't know. I also wonder how much of it was built around wanting to limit exploration with an AI character (since all the device did was kill you if Trip died or you wandered too far), which would be a shame since limiting movement and making Trip's death a fail condition would have been fine without giving me a story reason to dislike her. Interesting stuff.