I understand all of what your're saying, but none of that bothered me. With the enemy AI, yes, it is weak, and their dialogue is lame. That said, it's also a function of difficulty. If you crank it up to Survivor mode enemies, are smarter, more aggressive, and harder to sneak up on. Makes them a bit more realistic.
Being able to pick ammo off of every enemy would have made the game too easy as would enemies not having guns at all. So, it's an imperfect compromise. Didn't bother me.
The ladder plank thing I didn't think added any value at all. It didn't bug me, but I thought they could have made progressing more of problem solving exercise, as opposed to, where's the plank at, I know there's one around here. Missed opportunity to make the game better.
Story stuff:
Honestly, I think the majority of people (including myself) don't really know what sorts of injuries can be heal on their own. I understand that infection (hah) would be a huge problem, but aside from that, I don't intrinsically know whether that kind of injury would be 100% fatal. The one shot of penicillin was weak, but what can you do, the story needs to be moved along. So whatever, I got over it pretty quick. As far her moving Joel, I think that scene was necessary for the suspense. Assuming she was able to slow the blood loss (again, you have way more knowledge of this than joe average) she could have dragged him out of sight until nightfall, fashioned a stretcher and dragged him with horse. It's very much possible that she could have found a way to move him.
I honestly never noticed the supplies thing leading up to the hospital. I got there not knowing what to expect. I figured there would be more fighting to go, but I didn't necessarily think it would take place at the hospital. Possibly after leaving the hospital, I don't know, but it certainly didn't ruin my surprise.
Number 3 is a just a device to force Joel's hand. I agree that a culture should be all that's necessary, which is why I supported Joel's action. The fact that they needed to kill her showed a significant level of incompetence and callousness in my mind. If they're not even going to attempt to figure out how to do this in a non-fatal way, then fuck them, they lost their chance. So I totally get what you're saying, it just didn't bother me, it didn't snap me out of my being enthralled.
Last point, your recommended lie has flaws too, years later when there's still no vaccine being distributed what will she think? Why would word get back? Tommy hadn't seen a Firefly in years and Marlene was probably the only one who would have had a good idea as to how to find them. So, that one didn't bother me all.
It wasn't all for nothing because the story isn't about CBI or even finding a cure, it's about Joel, Ellie, and their relationship. All that other stuff was there to add drama and context. I think of the ending as a win because it was the right ending for the characters and their journey together. From the start, where Ellie is cargo and Joel is the smuggler, to Ellie beginning to care for him and Joel rejecting it because he can't let go of survivor mode, then Joel coming around to realizing that he does care and he's got nothing else worth living for. Ellie risks her life to save Joel, and Joel risks his to save her to seal relationship. She has become a daughter to him and he can't lose his daughter again, he just can't, so he finds a way to save her and try to protect her from her own feelings of guilt. It's the perfect ending to an amazing journey.
I think this gets into my "What type of gamer are you" thread, go there if you haven't. I think I'm just the type of person feels more and thinks less during a game like this. When I carried her to the elevator at the end my heart was in my throat. During the rebar injury and the slow journey out, my heart was pounding so hard I could practically hear it. When he's consoling her after the final encounter with David and calls her baby girl I started crying.
That whole scene, where she kills David and Joel arrives, when the sound fades and you're left to wonder what he's saying and you see her crying but nodding her head because she knows he's gonna take care of her. That shit right there is the single best scene in the history of video games imo.
Then there's just so much other stuff. So much of the dialogue throughout the game just makes me smile or chuckle. The scenes with Tess and Sam/Henry were gutting, the story of Ish and the survivors in the sewer I found really moving. Just, so much awesome. But it was all so awesome to me because of how it drew me in and played with my emotions, if it didn't do that for you, then I can see why the game would fall flat.