The amnesia is justified because a major mechanic of the universe is transferring memories. While the end sequence is quite messy, it's a much better commentary on the world it created than other shows trying to do the same thing.
Kaiba definitely isn't as bad as you say and definitely not as good as Petros says, but I lean on the good side. The episodic part of the show was excellent at showing how the world works when an idea is taken to an extreme, but the plot section is quite a lot weaker. The tree part acted as a good conclusion sequence but the bits leading up to that were incoherent for a lot of it.
Kino's Journey is Kaiba but without any form of plot or ending to act as payoff and with next to no character depth outside of several select episodes.
Well, at least Kino's doesn't promise any sort of progression or plot and perhaps not having any progression or plot is better than having a bad progression and a bad ending. But, yeah I guess my expectations were too high because everyone including Petros kept on saying that it was a great show.
If I had just randomly found it and watched it perhaps I wouldn't have been as negative. In Kino's you get weird extreme worlds each episode and you stay or leave for that. In Kaiba there is this mystery that in the end makes little sense. There just were too much ideas in this show. In the end I didn't get what this show was about at all other than some convoluted social commentary that is hard to put your finger on to keep it vague (like the artstyle) to make it hard to criticize its ideas.
Sometimes like in this case, I like or dislike an anime and then subsequently try to come up with reasons why I liked it or didn't. It isn't always that obvious.
"The episodic part of the show was excellent at showing how the world works when an idea is taken to an extreme"
It just came off as unfunny satire. I am fine with satire if it's actually funny like in Gulliver's Travels but here the characters(many of which especially in the episodic parts were extreme caricatures) were not funny or witty, nothing was made to be fun of. And besides the different worlds and the contant movement of the characters separately made it hard for me to empathize with anything that happened to the characters.
The constant misery-porn was off putting as well. I felt like I was being emotionally manipulated rather than appealing to my reason.
Kaiba wasn't satire. You seem to have been negatively affected by wrong expectations. It wasn't emotional manipulation because there was no manipulation to be had. It presented the full story in each episode, which generally was quite depressing. It would have been emotionally manipulative had the show focused on being sad rather than being honest about what would happen in a broken world where memories are physical.
SAO episode 3 is emotional manipulation because it presents a character, writes in that Kirito cares for her, then kills her off after skipping the process of coming to care for them. Kaiba never does this. I'd assume you find the Chroniko episode the most "emotionally manipulative", but this is very far from what it was. Warp didn't participate much in what was going on. He was apathetic for a lot of the early part, save where it directly involved him. You could say that the aunt feeling regret was emotional manipulation, but this isn't a strong argument because it's logical that an aunt would feel regret and guilt after selling her niece's body.
The amnesia makes sense within the plot but it doesn't help with characterization. I don't know. Warp was too apathetic for me to care about ironically I guess that makes me apathetic. I don't know, is that irony? So many things are called ironic that I don't know what irony is anymore...
I don't know it killed characters too fast. It gave me that same feeling I had when I watched Galaxy Express 999; 'Oh now you feel sorry for fictional people, give us your money, here you go another batch of characters to feel sorry for, now give us your money etc....' Perhaps I am being too cynical and perhaps this shouldn't be called emotional manipulation, after all that's the deal, but then what should it be called? Maybe 'misery porn'? I just find helpless victimized characters rather boring and 'manipulative' in the sense that they are just there to make me drip a tear from my cock.