A lot of what the league offered will not be coming to the main game; the map rerolling items, the core gameplay content, and the unique items are all noted as things that either had no particular need to be added or just did nasty things to the main game if added. However, the Orb of Annulment found a useful spot for crafting, and the associated language bits tied with lore will definitely be sticking around in the future. The league will also be available again from Zana in the future (albeit not in 3.1) so players can be assured that its popularity has been noted.
Path of Exile brought along the Harbinger league, and it turns out a lot of people liked to play that. More people than had ever played any previous challenge league, in fact. And considering the sheer scale of what was being released, it seemed pretty obvious that the Harbinger content appealed to people. So what do you do when lots of people like the content of a particular challenge league? You discuss adding things from Harbinger to the core game experience, obviously.
Source: Official Site