When you add memory protection to a system you don't just say "you cannot have process communicate", you give them the tool to do it in a safe way.
> You want to do it right, not quickly.
You want to do it right in reasonable time, otherwise by the time it is done it is obsolete. Given the time it took to add basic functionality, I would say that the design is not a good one.
In particular I suspect that the unstated premise was that everybody would be using Gnome by now, so that offloading to Gnome all of that functionality was a smart idea. Unfortunately people stubbornly continue to use the software that they like, so now we are in this situation.
> The final solution will be there for decades
There is no final solution, in 40 years the needs will be quite different that those of today, so it is not easy to satisfy both. You need an architecture that can evolve with the needs.
Remember the excel effect: each feature which was previously implemented by snooping and injection may only have a small number of users, but there are many of them and most users will use at least one of them. If you want to replace a system and not have users hate you, you need to implement all the little fiddly bits as well: my personal example is krita, which is not supporting wayland until it has support for tablets and qt has support for that, as well as color management (these aren't even things which were insecure on X11!). So for the forseeable future an app I'm unwilling to abandon is not even looking to start with wayland support until wayland has sorted itself out, and then it looks like it'll take them a few years to actually deal with it. And so it grates when I hear 'why is anyone still on X11?'
We see also arguing that something is missing, while it was there for years (like screenshots and capture), or nitpicking on global shortcuts. Global shortcuts are so incredibly long tail feature, so pointing it out is actually a a good thing. It means that Wayland is already here and nobody can find anything better or more important to point out (if it were up to me, I would agree with you on color management, but that is something that X never really had).
App support is something entirely different; apps like Krita can run under Xwayland just fine and transition on their own schedule.
On the other hand, Rome wasn't built in a day either. You want to do it right, not quickly. The final solution will be there for decades, so it better be not drag on maintenance and further development. Especially one, where the requirements are not so clear (no, register random key combo by random client isn't going to be it).