IMHO, separating MeeGo and Maemo 6 will certainly make the situation similar to android/symbian, "Custom/Cooked ROMs" as they are called with have Maemo 6 apps on the N900, with the license completely ignored by those making the images.

Oh and as for replacing Maemo apps with our own ones, I discussed 1:1 copies of the apps (as qwerty12 has done for one of the applets) on #maemo, but it might be a waste of work/time when the apps are already there, but the source is closed.