The question of what to do with Wayland seems like a question of how freedesktop.org and the X.org Foundation should interact. Those two organizations seem so closely related that I wonder if it even makes sense for them to remain separate, other than that they both independently have a great deal of name recognition.
X.Org works closely with freedesktop.org, as they provide hosting to X.Org and the related free graphics stack projects (Mesa, Wayland, DRI, etc.). The X.Org Foundation has been sponsoring work all along that stack, including projects for Mesa, Wayland, and DRI as well as the core/traditional X Window System, and the X.Org conferences include talks from all those projects as well.