Perhaps Skeletor, too, will get to move into some new territory. Just because the power of Grayskull is out of his reach won't mean Skeletor won't keep trying to conquer Eternia for himself.
If I recall correctly, there were a few occasions in the Filmation cartoon where Skeletor at times tried to DESTROY Castle Grayskull and it's power like the one episode where Skeletor traveled back in time to ancient Eternia where he was trying to construct some kind of fortress in the same place where Castle Grayskull was supposed to be in the present. With his completed fortress in it's place, Skeletor would've made Castle Grayskull cease to exist from the timeline. Kind of like a 'if I can't have it, nobody will' mentality with Skeletor for that one.
I think, in the new comic, Skeletor still will have plenty of motivation. First off, he hates He-Man for 'stealing' his 'birthright' plus all of the times He-Man defeated him. And, second, Skeletor will still want to conquer Eternia and lord over all living things. It just takes away the cliched 'Which Gimmick Will Skeletor Use This Time To Try And Break Into Castle Grayskull' idea.
Castle Grayskull could still function as a fortress of some kind and pretty sure the technology of the ancients would still be hidden within it's walls. I dunno, I just want to see where the writers take this new incarnation of MOTU.