In the podcast with Ziz, I believe, he said they're looking at removing 2 leagues. At the time he basically said it was going to be Prophecy most likely and didn't mention Perandus, but most people assumed Perandus or Talisman was the logical second choice. I think they did Perandus first because it's much, MUCH easier to integrate into the core game by just moving the Manor drops and that's about it. Prophecy will be more complicated, but they can just move everything to Div cards you can target farm to get upgraded items and shit like maelstroms and undead plagues and whatever they either remove completely or make a shitty fragment for the map device. I'd guess the former. Certain things like Atziri's Reflection would most likely be pushed to the logical boss like Uber Atziri.
There's other leagues that could easily be removed as well like Torment (ghosts lul) or Anarchy (exiles mean jack shit unless you've got IIQ and 20 of them or are SSF). The thing is I think for a lot of people Prophecy was a secondary league you had to interact with by using silver coins and a lot of people just stockpiled 700 of them and never bothered after they filled up with enough shit ones and didn't seal any. Prophecy farming was VERY lucrative if you had the stomach to do it, I think it was something like 3-5 ex an hour each league if you can actually make the trade for coins and the market isn't fucked with stuff like Vaal key Reflections.