I'll be answering the points one at a time as a gnome user so strap on for the ride, it's gonna be a long one. I'd highly recommend reading their post first so you can see the points which I'm adressing.
1. A Desktop that does nothing
That's part of the design, get everything out of the way. That's also why the workplace switcher isn't shown unless you press the user key. Maximimize screen real estate while still offering the features in a coherent manner.
2. Barely functional status bar
Sound is the exception because most people will simply use the keyboard keys unlike Wi-Fi or Bluetooth where that's not an option? That makes sense to me, I'm not sure what's off about this
a. Connecting to a Wi-Fi network is too many steps
From my understanding, this is done to avoid having an overly long sub-menu but still being able to quickly change networks (as opposed to opening the settings app which would be more work) It's a compromise made by design
b. No battery percentage option
This entry is misleading at best, you yourself admit that the option exists in Gnome Tweaks I'll explain why Gnome Tweaks is a good thing later ;)
c. No app indicators
This one is a little more complicated to explain. It's a good thing. Bear with me now.
First of all, the old format was the one supported by TopIcons, it's quite poor due to the API and so, they removed support for that old API.
"Okay but I want them!" I hear you say, that's why Ubuntu made the extension with a newer and better API which people actually support unlike what you lead people to believe when you say "Even if a better implementation may exist, it needs to be understood and accepted that cross-platform apps are unlikely to create indicators specific to the Linux Desktop, a marketshare of less than 5%.".
"Okay well, why isn't that in GNOME?", well, it's relatively new for one and well, it's more effort to maintain the more options you give but of course, that's entirely the reason why it's not done, it's also possibly because of design decisions
And that's where you comment on the GNOME-styled "Fragments" torrent client come in, that's the design that GNOME seems to want, "if you want your program to run, you should leave it open", and you might say that's terrible but here's the thing, GNOME is a very keyboard-based (more on that in a second) and uses Workspaces quite heavily so what you'd do is.. use them to put background programs if you don't currently need them or they're done for a specific "work" environment.
So about the keyboard oriented design of this anti-feature. What this effectively means is that you can use natural keyboard bindings to get to your application instead of using your cursor to get to the icon.
As for the intrusivity of the notifications, I hear you, I'd personally want a do-not-disturb feature to block the peeking as Pop!_OS provides, I think that's the best way to go about this issue.
d. No suspend button
Yeah, that's not great design and should be fixed, I agree.
3. Deceiving app drawer
You bundled things together here but I'll try to stay coherent in my response. First of all, keyboard shortcuts should be known, they're all in the settings if it really bothered anyone to have to click the application drawer icon in the first place... It's really the first time I hear this.
As for the truncated names, I don't really think this as an issue considering the icons are also shown but as you said, it's a WIP which will be done eventually for those that are bothered by it
The folder issue is real, I'll give you that but software handling it after a little of grumble works relatively well I would say.
4. Unnecessary notifications
That's done by design, windows are not meant to grab focus on gnome automatically, this can be annoying if you start an application then it just decides "lol, you were doing something? Well, I don't care, focus on me" and so it tells you that the application has sucessfully loaded in instead, I would not expect this to change. Use the extension if you want to be annoyed
5. Barebones file manager
a. Can’t create new document from the context menu
It's in the help documents, maybe use them. Although a default for a blank file might be useful. I'm not sure how you would want this to be more "intuitive"
b. Confusing action buttons
I think I'll be repeating myself more but it's by design, tooltips are not elegant and you misconceived the hamburger menu as a setting menu while it's an option menu since you wouldn't put 30 bajillion options in the titlebar, that would be a cursed sight.
c. Same icons for different file types
Can we not make an icon for literally every format on planet earth? Please. They're similar formats, let's use the same icon, spare my sanity.
d. Oh, the file picker!
Have you ever thought that GNOME devs aren't bothered by it and if people care so much about a stupid issue like that they could instead fix it rather than meme it? I think it's quite an hostile mentality to expect people to work on everything and then complain and meme the issue rather than trying to fix it.
e. Non-discoverable way to bookmark folders
Next thing you're gonna tell me that menubars are not intuitive and as per the issue you filed, we would like to not duplicate that UI since it's frankly not very useful to do so and just more clutter... and GNOME tries to avoid exactly that.
6. Document viewer (PDF reader) with no tabs!
The developer of the application doesn't want this by design. If you don't like it, there are other applications which you can use. Please don't force people to do things that they don't want because "People want it!". Thank you.
7. Two photo viewing apps
While yes, you could dislike that. There is a clear distinction between the two and maybe I don't want "GNOME Photos" to manage my photos but rather another photo manager but I still want a lightweight option like "Eye of Gnome" to view my pictures (which is what I do if you were wondering).
It's kind of interesting how you fight to get more options unless when you personally find it inconvenient..
8. Can’t find my settings
I know I'll hate this part.. but here we go.
a. Undiscoverable settings
Uncommon things are put behind 3 dot menus, who would've thought, right?..
Also, while you have ample of space, it's worth mentioning that most people can access more than 3 access points meaning there isn't as much place as you'd think.
b. Can’t set a custom wallpaper
Except you can and you just said so.. sure, a file picker would be nice but what you're saying is very misleading
c. Tweaks app that shouldn’t exist
I knew this was gonna happen... why..
Okay, so, yes, some options could be changed over. However, this is a design decision.. So, we don't want the clusterfuck of options from KDE so we put it in another application so those things are still available while not overwhelming the user which uses the settings application.
But there's also another thing to consider, some of those settings are not entirely safe to use so we might not want them to be as easy to access as all the other options to avoid the user breaking their system. Some options which could result in that include : Scaling, Themes, Extensions.
TL;DR : It's a compromise between flexibility and stability
Furthermore, gnome settings is more so DE-agnostic being that I could use all of the settings in there in another environment, while with Tweaks, that's not the case.
9. Software Center
These are just shown in the updates menu where you would expect them to be... Also, if they don't show up there, it's your distro's fault Conclusion
Even though I appreciate the time you've taken to state your points, I highly disagree and hope you can understand my points. Thanks for reading.