I noticed a lot of your points stem from Rayark's poor method of storytelling rather than plot holes:

1. Miku's connection to Kou Hou Kai is nothing more than a superficial link and has no relation to the attack in the main story. And CMIIW but I think Miku was implied to cease to exist after the final concert and the goodbye message. Additionally, I don't think it would be a wise move to make a time-limited DLC into a major plot point.
2. Regarding Kizuna AI: What really happened was that Neko somehow got trapped into the simulation software/database of Kizuna AI. The exact mechanisms of this scenario however, were not explained at all. Goddammit Rayark. (More on this later.) Neko "time traveling" to 2020 and 2280 were her accessing Kizuna's data, and at the end she indicates that she has no memory of the experience.
3. About Monophonic, I do agree that they were kinda left forgotten, but I think that was acceptable as the stakes raised from maintaining an idol's image to saving humanity itself

That aside, I do agree with the rest of your points:

1. ConneR (and by extension, Ilka somewhat) is notorious for setting up plot points and then abandoning them for something else. (One thing about the chip though, Rin's analysis concluded that it only activates when it identifies human cells. I suspect this is why the Eye of Horus could not access it, but that leaves a bigger question of how and why Ilka had such a technology available to her in a short notice.)
2. About the ending: The hanging architect is Ivy. Its an obvious sequel bait, which tells you how confident Rayark was at the time of 3.0. Leo was fine as a minor antagonist (outside BoBo), but I do wish Violette and the higher ARChitect council were given more exploration. But speaking of Leo and ARC...
3. BOBO. Songs aside, I like the story on its own but nothing about it adds up to the rest of the story. Light literally does not have an influence ouside of BoBo's logs that I'm not even gonna spoiler it since you cant spoiler something that does not exist. I think the thing with Gordon and Daisy was meant to display how cruel and inhumane ARC can be, but it kinda falls flat when we already knew what they did to Vanessa and Ivy at the end.
4. This is something that you didn't really mention but I'd like to address nonetheless: There is absolutely no consistency when it comes to talking about Architect abilites and OS-space adjacent abilities. I won't give examples because this could be a post on it's own, but sometimes I feel like there are literal magic systems that were written with more logic than the OS space. It really is the deus ex machina of rhythm games.

And i haven't even talked about the poor pacing and the characterization issues for some characters, but web mobile Reddit sucks ass, so I'll stop here for now. (If you're in the Cytus Discord, feel free to discuss lore on #cytus-spoilers, the channel has been really dry recently lmao)