You can do per-display DPI just fine on X11 (through xrandr), it's just the major toolkits don't support it. GTK, for example, reads a single global DPI value from XSETTINGS; there's no reason why it has to be that way.
The annoying thing about the other things you mention is that they honestly are not that difficult to fix.
The X server can throw an error (or just silently ignore it) when one client passes the window of another client and button/key events in the mask to XSelectInput(). And the Xinput2 bits that allow for receiving all key and button events can be changed to only send events destined for windows in the same client. There: input snooping is fixed.
Lock screen awareness can be fixed with new requests/events in the MIT-SCREEN-SCREENSAVER extension (or, if that's fraught, a new extension) that allow an app to create a "special" lock-screen window, which the X server will always stack on top, and send all events to. (That new functionality should probably allow for child windows and popups for input methods as well.) This is honestly not hard!
And yes, some applications will break when you do this. But I cannot see how that's not significantly better than creating an entirely new display protocol that everyone has to port to.
There are other issues with X11, of course, mainly in the graphics pipeline (e.g. the compositor should really be in the X server), but it's hard to believe these things couldn't be fixed. It feels like no one really wanted to do that: building something new from scratch that (in theory) didn't have all of the mistakes of X11 would be more fun, and more rewarding. And I get that, I really do. But Wayland has created so much work, so many thousands (tens of thousands? hundreds of thousands? million+?) of developer-hours of work for people that maybe could have been better spent.
So I think Phoenix is a great idea. It's basically "X12"[0]: removing the old cruft and making breaking changes to fix otherwise-unfixable problems. I imagine most modern, toolkit-using X11 applications would work just fine with it, without modification. Some -- perhaps many -- won't... but that's ok. Run a nested, rootless X11 server inside "X12" if they can't be fixed, or until they're fixed.
[0] Yes, I know that an X12-type thing was considered and rejected (https://www.x.org/wiki/Development/X12/), but I still think it's a better idea, after a decade and a half of Wayland still not being able to support everything we need to port Xfce's components and maintain all of their features.