I think the most likely candidate is one of the lighthouses. Venus Lighthouse, specifically, due to being the climax of the first game (
I have an idea for such a stage that I cooked up here). But my second choice would actually be Colosso: a scrolling stage that would go across various obstacles (with Garret, Ivan, and Mia all using psynergy to alter the stage from the background) before arriving in the center arena for a more traditional battle for a while.
I do agree that I think Venus Lighthouse is the most likely option. I really can't see Colosso happening because its just not that important to the overall storyline. I mean, yes, you're forced to go there, and it gets Babi's attention, but really, you already had Babi's attention anyway. As far as I'm concerned, Colosso just happens because they wanted it to happen, but its not necessary to the overall narrative.
The Lighthouses and Elemental Stars Chamber, though, are far more important. Since the Lighthouses are so central, Isaac is a Venus Adept, and Venus Lighthouse is the final dungeon of Golden Sun, it feels like the most logical choice. And if they do more than just focus on the roof, they can add a lot of unique mechanics by getting sand traps involved in the lower levels of the stage.
If they do focus on just the roof, though, I think they may add a teleportation mechanic, and it'd teleport you between each lighthouse, with a "Lighthouse" Medley as the main theme.