The thing with Egwene - at times, fortunately not all the time - is that she seems very strongly Mary Sue in the original sense of being a character who the author wants to be so great and perfect and better than the others, which just irritates readers. Especially in that infamous prisoner in the WT sequence, which seemed intended not only to convince the WT and Elaida of how superb Egwene was, but also the countless readers who had indicated their dislike for her.
So I consider her more "Mary Sue" than any of Eddings' characters - Polgara has a certain "practically perfect in every way" aspect to her, true, but she's modest and far from showy about it (except, again, in her own series, where her impetuosity and resentful temper make her rounded enough). But yes, obviously the comparisons you make make far more sense in terms of roles and characters. And yes, RJ does do a better job - I too have too many fond memories of Eddings to attack him too hard, and still enjoy rereads if not as much anymore as I once did, but his characterization is not too great even by the standards of Robert Jordan or other contemporary epic fantasy writers.
There's a certain similarity to the pair of them, though, when you start thinking about it, in terms of how they characterize women and gender relations - the old-fashioned aspect of it, the notions of women being almost an alien species who conspire to confuse men, and men being pretty much helpless once a woman gets them in her sights, that sort of thing.
True. As a protagonist, Belgarion really doesn't do much on his own - most of the time he has either Polgara or Belgarath, or a lot of the time both of them, to guide his hand. And even when neither is there, like with the Zakath scenes, he still has the Orb. And the Prophecies.
I thought the attempts to balance Sephrenia worked out alright, actually, though admittedly it's mostly in the Tamuli - with the racial tensions issues and the greater emphasis on her not being without mistakes in her love life. In the Elenium, it's only really Aphrael who cuts her down to size once or twice.