Obviously they don't have to pick between something they have done before.
They would do what would fit the situation.
In case of Hoenn, of course a "BW2" doesn't make sense, unless they pulled some silly forme business on the main legends...
But a Johto-like.....bonus generation for Hoenn, would be quite interesting.
As its been so long, they wouldn't even need to make up a second connected region for that, as Hoenn is reasonable to have changes and new places a decade later.
It sounds like an obvious "beating 2 flies with one strike" case to me.
They would milk the Hoenn nostalgia, but still be offering a new game at the same time.
So in short, with sequel I mean anything between the "BW2" and "Johto" concepts.
It wouldn't really milk the nostalgia unless they had both the original and sequel released(to bring Hoenn, in general, out into modern standards; the only region yet to see this), only the former would really bring that out.
I admit that I didn't think about what you are mentioning though; that could have potential, although I doubt they'd be that distant in the future(real time has little to do with game time in this case).