I quite like the worldbuilding, but I had the same problem of not liking the characters. Enough so that I didn't bother reading the third book. Part of the problem, I think, is that what I was willing to give Lyra a pass on during the first book as childish bad habits she'd outgrow in the course of the story, by the second book were being shown as her most useful and stalwart qualities that she should be proud of. Which may be me reading too much into the author's intent, but it did come across that way.
I think part of what's going on in Pullman's trilogy is that he's more interested in making certain philosophical points about independence of mind and standing up to authority, and less interested in making the characters into people you'd want to actually know in real life. Also, notwithstanding the fact that Pullman has claimed, in at least one interview that I read, to be interested in telling good stories above all else, I don't see the storyline as being the element upon which he concentrates the most in the "Dark Materials" trilogy.
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