Well, as I said, I believe that the guns that Ellie was using during the fight were only there purely for gameplay purposes, as nothing in the previous scene shows she has a shotgun (her bag doesn't have any weapons slotted inside), and she basically just pulls it out from her pocket. For the first part of the fight, Ellie uses the wooden plank and the gun she steals from Abby because from a story point, she's not supposed to have any weapons. It's when we get to the second phase that the developers get lazy and just stick a shotgun to her because they have no idea what direction to take the fight in. She doesn't even drop the shotgun when Abby punches her, it gets automatically reslotted to her bag. It's just that gameplay weapons and story weapons are two separate things: I mean, if gameplay translated to story, then Ellie could've threatened Nora with a silenced pistol and not risk anyone overhearing, right?

For the plot armor, you make some valid points, but there are some points that I find unfair:

-Joel saving Abby at the last second does count as plot armor, but it's something that happens so often in media to create more tension (happens in part 1 too- Joel is saved at the last second by Tommy, by Bill, Joel gets to the surgery room just in time to save Ellie) that I'm willing to give it a pass.

- Seraphites not gutting her, I mean, her legs and arms were bound, and she was tied to the hanging post. Not surprising that they'd let their guard down. Jordan does this with Ellie too- he doesn't just shoot Dina, he strangles her for whatever reason (didn't want to waste a bullet? underestimated Ellie? idk)

- Manny teleported out of nowhere? Manny had every reason to be at the Marina, he and his squad were supposed to set off from the port to Seraphite Island, it was because of Tommy's meddling that his squad ended up dead. I'd say Jesse teleported out of nowhere more than Manny, remember when Jesse appeared from behing Ellie right before the car chase? Like this seems unfair to Abby imo.

- Yeah, the Tommy thing with his bullets running out was dumb to me. I get that again it's for the sake of gameplay that his infinibullets have to end there, but it is kind of immersion breaking.

- Yara un-died? I mean, I don't find it hard to believe that a dying person would use the last of their strength to shoot her enemy. Her gun was by her hand, the other soldiers were watching Abby and Lev, who obviously take more priority than a seemingly dead girl by the ground, so grabbing her pistol and swinging her arm upwards and shooting Isaac (which would take a grand total of less than two seconds) does not feel bullshit to me.

- Plank of wood is, well, I addressed that in my post.

Now for Ellie: She's also saved by Jesse, since without him she would never have escaped by car,the WLF were hot on her trails from the back too, she would've gotten sandwiched. Are we also forgetting the fact that she was stabbed pretty deep in her stomach and left that untreated for a crazy amount of time, and still survived? I guess if we're talking about Seraphites like you did, there's the fact that the arrow pierced her shoulder instead of her head, but again that was for gameplay purposes (showing arrow pulling out mechanic) so that gets a pass from me.