Bill Spitzak along with Pekka Paalanen and others have begun hashing out the design for the Wayland compositor to control window stacking and raising. This is now being discussed in the public on the Wayland mailing list.
As far as a summary, "The basic idea is that clients must request raises of their windows and that windows are not reordered except when this happens. However the raise request contains multiple windows. The compositor can still overrule this and has a clearer idea what the client is requesting."
Other key points for Wayland window stacking / raising is that the compositor's immediate raising of windows upon clicks is an un-workable design, handling of full-screen applications with desktop panels, raise notify events for Wayland windows, and the design of raise request events for the Wayland compositor.
See the email on the Wayland mailing list and the follow-up messages that are discussing the different possibilities.
In related news, new Wayland full-screen mode patches were published this week. Jesse Barnes also updated the plane handling support, among other Wayland patches floating around by others. Wayland development is beginning to heat-up.