Doll's article is built on the premise that Katniss (of The Hunger Games fame) may be a revolutionary character in American film, but not in literature. It's a noble (if altogether warped) premise, but the execution is clumsy at best. What I'm bothered by is the fact that Doll's list is almost exclusively comprised of very old characters, with only The Book Thief as a remotely modern book. Not that these choices are necessarily void because they're old, but this is certainly not the list that I would ever come up with.
At Tor, meanwhile, Ness unsurprisingly comes up with a different list entirely and opens the floor up to nominations. As I read through the list (and subsequent comments), I was struck by how different the two approaches are. Half of Doll's heroines live in a society of young women who seem forced to exceed society's expectations, while the other half are simply well-characterized girls. It's all very reality-grounded. Ness' choices and the majority of the choices listed in comments, meanwhile, predictably lean in the direction of fantasy. Many comments name one of my personal favorite characters Lyra Belacqua (of His Dark Materials), and Ness specifically addresses another unacceptable omission in the form of Hermione Granger, who despite not being the main character of Harry Potter is definitely a main enough character to justify appearing on any list of this kind.
I have my own lists of great characters (girls or boys). I've already discussed Leslie Burke, and I can certainly discuss Hermione or Lyra for hours at an end. And I have to admit that I was thrilled to see one commenter add Antimony Carver of Gunnerkrigg Court to the list, though she's only one of many wonderful girls in the story. Others: Ella from Ella Enchanted, Cimorene of the Enchanted Forest Chronicles, obviously Meg from A Wrinkle in Time (thankfully included in Doll's original list), Coraline from Coraline, Tamar from Someone to Run With (my own addition), and many, many, many others. This seems like a field worth delving into further.