I have only read The Belgariad, The Malloreon and it's sequels so I cannot speak about his other work, but I have always been pleased with Eddings' (and I guess I mean both Mr. and Mrs. Eddings') versions of female characters.
I guess I am slightly (or extremely) odd though, because I happen to LOVE Ce'Nedra (I do, I think she's extremely well nuanced character) but I think in females (especially when written mainly by male authors) tend to either be "damsel-esque" or "kick ass-esque," even in extremely well-written fiction (novels, films, television shows) it's hard to find women who are all the above and more, and shows with such characters still include the extremes (though in those, the extremes are more tolerable). I think the Eddings' did a pretty darn good job at illustrating female character with positive and negative qualities.
I'll use Ce'Nedra as my example since she seems so unpopular, yet she's a character I love. She's spoiled, bratty, condescending, manipulative and very many other negative things, but she's also smart, loving/caring, determined, loyal and extremely charismatic. Whatever it was that brought the army together, seems to work on a personal level as well since despite her mood swings she's so easily able to make friends of other women.
I think that many female characters in this series seem unrelateable, not necessarily because they are badly written, but because of the window through which we see the characters. Other than Polgara the Sorceress and the few sections in which we are reading through Ce'Nedra's perspective (the sections in which we actually see much of her motivations, and are shown her fear of losing her identity which is probably something she's feared all her life...even marrying an older Tolnedran, at least she'd still have her identity, marrying a King of another nation could make her lose that easily, and as someone who was raised not to bow to others, male or female that would be frightening) we look through the eyes of male characters. And while in some respects there is something "modern" about the women (I don't think so, I think strong women have always existed, even in extreme paternalistic societies) there still seems to be a degree of segregation between the sexes. In my humble opinion, it's often easier to relate to the male characters because the male protagonist himself does not often understand the female counterparts. He relates to the males, he hangs out with the males, while Polgara raised him and he trusts her above most others, he's still able to learn more easily from the males (or those instances are shown in more detail, he seemed to learn to write "off the page" and many of his discussions with Polgara also seem to be "off the page").
Garion seems more comfortable with males for many reasons, the inherent segregation between men and women for one, and also because he was raised by such a strong, controlling and even meddlesome women. For instance, perhaps he tends not to challenge Ce'Nedra is because of how and by whom he was raised. After all some studies (I don't have citations, sorry), boys raised by strong, stubborn women tend to marry strong stubborn, women and women raised by strong, stubborn men tend to marry strong, stubborn men (This is why it's concerning when straight boys have abusive mothers, or straight girls have abusive fathers).
Anyway, I guess to summarize my post (sorry it's so long) I don't think it's that the women are actually badly written or unrelateable, I think it's that we are "seeing" them through extremely biased and well confused eyes. When attempting to decipher the female characters with that in mind, I think they tend to be extremely relateable, interesting and well-written (including and especially Polgara and Ce'Nedra). His characters in general aren't the deepest, but because of his tone, there's so much potential depth in the characterizations.
Eta: Yes, I know that The Belgariad and The Malloreon are written in third person, but they are still for the most part usually slanted towards the perspective of one character or another (if that makes sense).