Just finished it last night myself. Winter was awesome, and I actually quite liked the ending.

Originally Posted by
NeoCracker
(SPOILER)I thought the end was great... Kind of.
What got me was the Fireflys had been doing this for a while, and made no progress, yet kept at it. (Mind you, it could have been a lie from Joel, but at the same time it makes more sense that he was telling the truth. I mean they discovered the mutation and plan pretty god damn fast, and decided to operate that soon? They had to have done this before.)
What kind of kills the ending a bit though was that no one took any kind of believable action. Hey, there's a guy trying to resusitate a girl! Let's knock him out.
Hey, there is girl I've practically raised as a sister/daughter! Let's sacrifice her to research that has consistantly failed horribley!
Hey, there's the guy who just gunned down god knows how many of our men! How about I not take this clean shot at his face!
I actually somewhat disagree with you here, but here's my reasons why if you're interested:
(SPOILER)- I really don't get the sense that the fireflies had done this before. I believe one of them makes not in one of the tape recorder messages in the hospital that they never saw anything like that mutation before. Now maybe they'd seem different levels of resistance before, but I doubt that even if this mutation was fairly common that people with it would survive long between infected attacking in groups, humans killing people who are bitten on sight, and just the general nastiness that can happen if a bite gets infected. Might be wrong, but that was the sense I got. We don't really know how long they had Ellie there doing tests either, but it's possible they'd been preparing for months before they all got there for what tests they'd need to run, ran them fast enough to determine they couldn't get the parasites out without killing her, then jumped to surgery. It is kind of fast though and probably just an excuse to have Joel need to kill their way out of there and save her.
- Knocking him out I get. You don't know who he is or what they want, knock him out, resuscitate the girl yourself and figure out what's up later. It'd be more prudent to kill them on sight to be honest, but they probably settled for knocking him out just in case since he didn't attack them right away and the girl needed help.
- You can actually find her journal in the hospital and she mentions showing up at the hospital without Ellie and thinking that she's probably dead. She ends up feeling ostracized because she lost the only hope they had for a vaccine and talks about not being able to take it there after a few weeks and possibly leaving because she can't stand how the other fireflies look at her any more. I'd imagine that that played a big role in her decision once Ellie turns up, not to mention her being the best hope of finding a cure. I'm not saying she made the right decision or even a good one, but where she's coming from is a bit more understandable in light of that. She's torn between her promise to Ellie's mother, her hope for a cure, and her original feelings of failure. Once Ellie shows up again it's like she was given a second chance to do what she originally set out to do. I think it's somewhat interesting to wonder if her decision would have been different had Ellie and Joel made it there at the same time or before her.
- Are we talking about after he picks up Ellie and runs for it? I thought it was weird at first but they may have needed her alive, or at least couldn't risk shooting her in the head or anything if they were going to be successful and get uncontaminated samples. They do open fire though when he's trying to get in the elevator and could potentially escape. In fact, I accidentally took a wrong turn the first time I attempted that sequence and one guard grabbed me while another grabbed Ellie and took her away before a third put a gun to Joel's head, so they really might have wanted her alive until the surgery.
Anyway, I'm not saying your interpretation of a lot of this stuff is wrong or anything, this is just what I took from it based on some information in the hospital and the behaviour of the NPC's.