Honestly? I think its mostly that as the scope of our lives expand and our everyday begins to encompass a more global set of cultural norms, we are more open to questioning what it is, exactly, that defines a person's "goodness". As our global society grows, we find more and more that a traditionally Western set of morals is not only not the be-all-end-all of what a "good guy" can be, it is often actually a rather narrow and undesirable state of being. I think that many people see a characters like Wynne and Alistair as being fundamentally incompatible with a broader mindset because they have very traditional, clear-cut values in some senses, and this makes them feel put off by the characters. (Just speculation, btw; I know diddly about anthropology and probably even less about psychology.) Those thinhs are not necessarily true about the characters, but its really not too difficult to understand why some people find (for example) Alistair to be a bit of a whiny man-child, or Wynne to be the preachy school marm that Morrigan accuses her of being.
Personally- I love both characters precisely because they seem so, well, human to me. They're set in their ways and ideas about some things, open to change on others, and can also let their emotions take over and become childish, bitchy and irrational about some things. Its no secret though, that I love the "bad" or at least, morally ambiguous, characters like Zev a little more than the "good guys" however. For me, a "bad" character seems, not necessarily more realistic, but more in tune with the way that I perceive myself. Whether it be sexual misadventure, social awkwardness, trouble in school, or a tendency to be overemotional, most of have issues (or have had issues) in real life, so maybe its just easier to relate with characters who are also so obviously dealing with their own **** and making fulfilling lives for themselves regardless.