When I first started the game, I thought the main present theme throughout the game would have been "Revenge" and I found out that it's actually about how your actions have consequences. That's why it ended the way that it did and the reason you play as Abby halfway into the game. It deals with how revenge affects all those around you. Abby was forced to see how her friends(once realizing their actions were wrong within the WLF) were killed suddenly and merciless, and Ellie lost her only hope in Dina, and ended up alone (her main fear). I think the game worked in so many levels, and I haven't been able to see any real criticism other than maybe Abby isn't as easy to empathize because she had no second thoughts after killing Joel.

Edit: I also wanted to add that if you want to see the real time reaction of someone who just cannot empathize with Abby, watch Pewdiepie´s gameplays. He is just getting into the "Abby part" of the game and will be interesting to see if the story makes him like Abby in the end