I guess it all depends on timing. 2020 is 3 years away (The usual length of time from groundbreaking to opening for a theme park). It just doesn't seem to make a lot of sense to sacrifice an existing attraction to shove a new headliner IP into a park that's already doing pretty well. One it takes something off the table that could be a big draw to the new park and additionally offers relatively new competition to said new park. There were pretty strong rumors of this several years ago (Kidzone was supposedly closing in 2014), to me it almost seems like they put it on hold to see if they could purchase the new land. Now if the plans for a new park have been scrapped or delayed then yes I could definitely see Nintendo going in USF. They could have easily closed Kidzone and E.T. months ago and gotten started instead they're doing refurb work on it. I suppose everyone is entitled to draw they're own conclusions, I'm just not seeing it from a logical standpoint.
ET has been the oldest. But, it may be in a similar dilema to Revenge of The Mummy, where time is of the essence, not because of popularity; but because of the technology of the ride system in-place, and GSAT's.
They could very easily be pursuing the same strategy as the Wizarding World. Universal Studios has The Wizarding World of Harry Potter - Diagon Alley and Islands of Adventure has The Wizarding World of Harry Potter - Hogsmeade. Universal Studios will have Super Nintendo World - Mushroom Kingdom, and Site B might have Super Nintendo World - Hyrule.
That's the way I think/bet is happening. Super Nintendo World's first phase, is of The Mushroom Universe, consisting of Mario; Donkey Kong and Yoshi, as they are all connected to the same universe.
Then, you can easily have it be said of Super Nintendo World at Site B being of the Hyrulian Universe. What they would use, in timeline's; depends.