I don't remember any glaring plot holes after playing through it and I got nearly every story related data point. I liked the story myself in part because of how complete and thought out it was.
I'm open to being corrected and/or informed, but there are quite a few things that I am bothered by. I read every text log and listened to every audio log I came across. It's not that I don't think it's a cool story, but I think there are too many glaring issues that just kind of ruin it for me personally. I'm sure some of my interpretations are subjective, but here are some things:
-Why do so many of the new animal machines have such crazy defense mechanisms if they are there simply to cultivate life and build the new earth's systems? Do they really need lasers, guns, crazy melee abilities, etc?
-How the heck did Zero Dawn's new animal machines even stay in existence without resistance of the "bad" machines? If the "bad" machines were gone when the new ones came around, I don't understand how they were gone in the first place. The tech in this world seems to be powered indefinitely, if not for a very very long time. Some of the tech from before the crisis is still powered on and working, so it doesn't really add up to me.
-There are so many huge carved out under ground systems just for the old world and Zero Dawn. Where did they displace so much dirt and stone and how could they possibly do that during the dangerous context of the world crisis? Seems outlandish.
-How does Aloy know how to perfectly interact with the old tech right away? I really hate how nonchalant the game is about it. She just waves her arms and hands around and perfectly does it.
-The entire concept of them coding an entire AI that is capable of not only simulating the earth and all of its systems, but capable of simulating emotion and empathy. The task alone of doing such a thing, including storing all relevant data in order to do this, seems completely ridiculous. They did this incredibly advanced thing in a short time, but somehow couldn't crack the code/glitch/hack that the machines were using on the surface.
-The idea that the machines were programmed to use biomass as an emergency energy source is a convenient plot point to set up sci-fi Armageddon. Look at how all of the "old world" technology can just sit there dormant for so long with lights and monitors and computers working properly. They don't need biomass, they just keep running. Seems they have perfected energy sources to keep things running for a very long time, without the need for some crazy dolphin slaughtering biomass meal (from a text log) to keep running LOL. Also, the machines can create other machines on a "as needed" basis, so the idea that they even needed an alternate energy source is just goofy.
-I really hated how there are these secret ruins, but the game throws human enemies at you that somehow just drop from ceiling vents in rooms behind locked doors that you have to solve to open. I rolled my eyes so hard.
-Apparently you take down the "focus network", but can still communicate with Sylens after doing so. LOL okay. If you want to argue that it was just for the villian humans, the game should have told me so. And if that is the case, how did they create a private network when they don't have much understanding of the old tech. Hades just magically assists the bad humans it seems.
-I found the Nora tribe to be incredibly stupid. Felt like a set up to make you compare them to ancient tribes, but just because ancient tribes believed in various gods that controlled nature, doesn't mean they would react to a giant metallic door that says the same thing over and over. Aloy even walks through it and the people could clearly see into it and it was just a bunch of rooms with ancient tech. You could argue that their reactions are plausible, but it's just not fleshed out in a convincing way to me. Especially considering the matriarchs are only allowed inside one of the ancient ruins in the mountain. The fact that the "old mother" was the one that delivered Aloy in the mountain next to the door, but the tribe rejected her is just so strange.
There's more I could say and more I could nit pick, but it's probably not worth it.
I haven't finished the game (near the last mission), so maybe some of this stuff is explained, although I really doubt it. I just feel like the story has too many questions up to this point and it's starting to hurt my enjoyment. It didn't help that I called the plot set up after the first 2 hours of the game, so by the time I got there I just chuckled. It's a story that is fairly well told, or at least written, from a human character point of view. Just not sure it works as a whole.