s5134195, don't forget that the island its self is subject to the will of the Psijic monks so it could be constantly changing. From different seasons to completely different geography.
Great point!
Maybe throughout the course of the main story quest, the island could make sudden movements around Nirn.. Or even into daedric realms, changing (as you said) the surrounding geography and overall ambience of the place. Finally returning to Skyrim in order for the Dragonborn to depart. I like it.
I think it is key that the Psijic Order showed up to retrieve the Eye of Magnus. While I do not doubt the the range of the extreme magical power of the Altmeri mages to teleport between the island and Skyrim, I think them moving Artaeum in proximity to Skyrim during the transfer of the Eye is relatively believable, for convenience's sake. Also, they may desire the Dragonborn's aid in dealing with the meddling Thalmor, who have mysteriously been able to infiltrate the island's secure whereabouts. Now on Artaeum, they are becoming increasingly difficult to dislodge without arousing larger powers, and have become entrenched in a deeply political siege. The Dovahkiin has proved useful in securing the Eye against the Thalmor.. His/her services could be called upon again.
Also, I think an island is about the perfect size for an expansion/dlc. One region limited in size and one new city is what Shivering Isles had.