Making you play as her just felt contrived. It would have been cool if Ellie and Abby had been thrown together, with them not knowing who each other was. They could have been a duo escaping a common enemy (the cult), and then suspicions slowly arise between the two before they realize who the other is.
It was hard to sympathize with Abby as a player since she didn't exactly have the moral high ground. Her dad died after trying to hold a knife up to Joel who was trying to save his daughter, right? That's not equivalent of turning Joel into mush in front of Ellie.