-Adam and Eve are an attempt by the network to understand humans by emulating them. The terminals outright state this to 9S.
-The copied city is Adam recreating a human city. He says this to 2B immediately after she arrives there.
-Androids are made in factories or pieced together by other androids. YoRHa androids are made in the bunker.
-Eve's skin is literally just a visual indicator that he's angry. I'm not sure what you were expecting, or why you assumed it was the black scrawl.
I honestly have no idea what more you wanted. All your examples are explicitly explained in main story cutscenes.
Which isn't to invalidate your complaints, but I'm curious why exactly you feel like they aren't explained enough, since others have said similar things.
That's the reason for Eve's skin? Wow. I totally made an incorrect connection based on my vague recollection of Nier 1.
Aside from the terminals (which were the red dressed girls, right?), your answers don't really go to questions I had. But that onus is on me for not being clear enough with my issues. For me, the issue was more so the story telling rather than the story and themes itself (which I actually enjoyed). What I'm trying to essentially say is that I dislike how I had to construct so much of it or piece it together outside the game. Not necessarily because aspects are not explained, or because the world doesn't make sense but because I don't think the game tells the story well enough outside the core conflict and that left me a bit hollow having finished it.
For me, I think the game needed to be a bit more concise with its main story to be effective. I was actually quite bored with the first repetitive half of route B and maybe that contributed to the story not resonating with me as much (I beat route A within a two days but took over a week to go through route B). Simarily, the way certain story beats were executed did not resonate with me at all even though I think they should have. And I'm still trying to nail down why.
2Es death for example didn't do much for me when it happened. Maybe my expectations and assumptions of where the story was going played a part? I thought at the time we'd get a bit more of her via 2A, another model like her, a flash back or something but that wasn't what really happened. So when I finally understood that 2E was done and there was no more of her , the moment had already passed and I missed that opportunity to resonate with that particular death scene.
I dunno, it's kind of hard to explain I guess. I resonated quite a bit with Pascal's story line. Probably the most out of anything in the game and that's one of my favorite gaming moments. So if I had to give an example, maybe that level of execution is what I was hoping to see out of some of the other plot lines? It felt more concise, more focused. The way it was told made me resonate with the story much more. Going up to Pascal after the memory wipe and having her not recognize 9S was a fantastic moment. And I just never connected much with some of the other plot strings and characters in remotely the same way.
Hopefully that clears up some of where I'm coming from. It's hard to pin down as I myself parse my thoughts on the game with regards to why I felt that way given the medium of gaming and how many factors are in play.