I used to be a die-hard Twilight fan. (see my username. Damn I wish I'd chosen ANYTHING else sometimes.)
I still like the book in small doses now, and I even write fanfiction for it, but now I've looked critically at SMeyer's characters, and I think I realize what people are talking about when they say Bella Swan is a Mary Sue.
As a person who has seen it from both sides, I'd like to say that maybe Twilight fans didn't see Bella like that to begin with because she has so many "flaws".
I'm not really a mega-supporter of Bella's neediness. And I even, admittedly, wonder why she took Edward back after New Moon. Normal people with lives and better things to do would say, "Hell no am I taking you back. You left me crying in a forest, and you think I'll just come running back to you? You wanna commit suicide, go right ahead while I get the popcorn."
I still like Twilight. But maybe Bella Swan was kind of 2-Dimensional.