Gnome does some questionable things, and some are just personal preference, but there is at least one thing that they do that makes zero sense regardless of how you use your system...
The AppIndicator extension SHOULD be default. There is no reason for it to be an extension other than pure stubbornness. There are applications that literally require it in order to function at all.
That you need an extension to disable the overview at startup still boggles my mind and the arrogance of the developers in the thread that started it didn't lessen my antipathy for Gnome at all.
It provides easy access to search. I understand now though why you wouldn't want it to open automatically (if you have startup programs you want to see instead).
In my case because I have my PC connected to the TV and Steam starting automatically in big screen mode. But according to the devs I'm doing it wrong and should get used to it because it's the better experience when I can go and grab my keyboard to start typing the name of the program I want to start.
I'll be honest, I could probably use Gnome if I had to, with a few addons. But when I try it, the second I get to that dialog and it does that, I just shut it down and install something else. To me, it just epitomizes the contempt the developers have for the users, that it continues to exist after this long.
There's a new Wayland protocol that probably will land in the next gnome release. The new protocol is supported by KDE and other desktops as well.
The reason that it was removed is because it is extremely hacky and bad. There have been talks within the project to just reads support since the extension got so many downloads but the new API is better anyway
I won't disagree with you there. They should've had a replacement before deprecating it. In there defense there was a alternative being developed but it ended up stalling over disagreements between KDE and gnome. The whole thing is a dumpster fire honestly. I'm glad they are cleaning it up. KDE and Gnome want the same thing for the most part they just kept getting into pointless bickering.
"I understand that some compositors have no interest in allowing clients to show arbitrary content in tray areas. GNOME, for example, doesn't even have a tray area and it is my understanding that they believe that even the current SNI protocols allow clients too much freedom. Such compositors should not implement this protocol."
--the page you're referencing, by the creator of the protocol
Gnome also believes that a window must have control over its own titlebar to draw it as it sees fit while simultaneously declaring it must not have control over a tray icon.
Also funny that Gnome seems to have objected to KDE proposal and wrote their own even though they seem to say point blank that while they are dictating how all the other DEs will do it, they themselves will be ignoring it. Why get in the business of a protocol you don't even want to implement in the first place...