Speaking of Best Pony, Twilight's studies seem to be very broad. She doesn't appear to be a PhD or a graduate student working on only one topic. It could be that she is the go-to pony for theories and application in friendship, but I've always seen her as one day returning to Canterlot for her studies of all things. Again, Ponyville isn't far away from Canterlot, so she could study during the week in Canterlot, and then return to Ponyville over the weekend. She studies late into the night, so it is less likely that she would commute than Rarity who would clock out at 5ish to take the ride home.
I say that Fluttershy and Pinkie would stay for the same reasons. Their special talents involve making some creature happy. They've both created genuine relationships with their respective realms, so moving seems to be out of the picture. However, I'd say that Pinkie might be more likely to move, because Pinkie can find other ponies to make happy. Technically, Fluttershy could as well, but she's more concerned with taking care of the animals. Pinkie could go to another city as long as she knew the ponies in Ponyville were happy. Fluttershy could technically take care of other animals elsewhere, but who would take care of those animals if she left?
I can't really make much argument as to why Applejack would move. She loves her family, she has an established and successful farm to work on with her brother for a long time (both of which have related cutie marks,) she loves helping out the pony folk in Ponyville, and she's very traditional. If she moved, then it would be under unfortunate circumstances; none of which would likely be done in the show (e.g., farm fails, she turns on Ponyville or vice-versa).
So yeah. There are four tiers of likelihood of relocation. I think Dash (sleep and ease/speed of travel) Rarity (being suited for Canterlot, being close to Ponyville) would be most likely to move. Twilight (late nights of studying, being close to Ponyville) would be likely to move at some point, I believe. Pinkie would be that third tier (she can make ponies happy anywhere). Fluttershy and AJ have too much keeping them in Ponyville. AJ has more structural ties to Ponyville, so I'd say she'd be a little less likely to move than Fluttershy.
So:
>Rarity would be most likely to move.
>
>Then Rainbow Dash
>Twilight and Dash may be interchangeable in likelihood.
>
>Pinkie Pie
>
>Fluttershy
>Applejack
As for the Elements being together, Unknown, you make a good point. I don't think Equestria anticipates such disasters, but it does have it's "friendship nuke" should she need it. However, remember that the Elements are not restricted to the mane six. This is where they lie currently.
As far as we know, the Elements were discovered and used between Luna and Celestia. They likely stayed with the two until the initial Nightmare Moon incident, and Celestia was able to wield them well-enough without her sister to banish Nightmare Moon.
I'd like to believe that the Elements became inert after this, because Celestia lost her only friend.
But they were never seen over the course of a thousand years (again according to what we know of the history of Equestria) until they were needed. If there are no more disasters that merit the use of the Elements, then the Elements' wielders could become someone else who could properly exhibit all of the attributes of the Elements. Heck, it could be the CMC and each of the three exhibit two attributes.
However, your point is valid. It would certainly play into the minds of the mane six before they moved.