That's not a Wayland problem. The features you're asking for are probably still there but they're implemented at a different spot in the stack instead of trying to stuff everything into the same protocol like in X11. This is actually done to reduce fragmentation. Make a service its own daemon with a dbus interface or something like that, and then it can run the same on X or on any Wayland compositor.
In my experience it's actually the simplicity of building window managers in X11 that's misleading. It's easy to get something up and running that lets you move windows around, but to build a full desktop that does everything you'd expect is a giant task, and X11 only really gets in the way of that.