We now have Wayland well on its way to replacing X(I'd say within two to three years, some users won't ever know they're running Wayland), and from what I can tell, it will offer fairly good isolation for input.

Another important step is graphics drivers being cleaned up to improve isolation between graphical clients. For the time being, though, I can create a GL context and not draw anything, but still see parts of the framebuffer in my context, which I find giggle-worthy.

I think the basic problem here is that graphics systems are hard enough to make work at all, let alone make secure. I will probably not trust a system this complex to protect input or content for a long time, if ever.