In my opinion the main idea is that both Ellie and Abby have the same motivation and neither is in the right.
Which is a retarded take Druckmann keeps insisting on, despite the whole of the first game deconstructing the myth of the "resistance" and depicting the Fireflies as a bunch of morons with no actual clue what they're doing.
Even the good doctor (which I doused with the flamethrower) had no actual idea if cracking Ellie's skull like an egg would lead to anything. Let's not forget that Ellie wasn't the first immune person the Fireflies had found and killed.
So not only are they not getting anywhere with finding a cure, they're actively culling the very people that do have an immunity and could pass it on to their descendants. If they were actually committed to solving the issue, instead of LARPing as post-apoc Antifa, they'd set up eugenics programs to breed as many immune babies as they can get away with.
And as others have said, what chance do the Fireflies have to find a cure compared to FEDRA and all the resources at their disposal?
Also, Abby is a detestable character, and nothing in TLOU2 makes the audience warm up to her. The retcon attempting to justify her murder of Joel feels tacked on and hollow.
If Druckmann had really wanted to pull the Jewish "both sides bad" shtick he should have devoted the whole second game to Abby, only revealing who her father is either at the end of the game, or in TLOU3, and having that game focus on the dual protagonists and their simultaneous quests for revenge.
Not that I think it would have worked out, but I'm also of the opinion that TLOU1 had no need for a sequel and there was frankly nothing a sequel could have added to the story of the original.