Here's a few confirmed ones (based of questlines from Heritage Armor quests, Allied Race acquisitions, and other additional questlines):
- The Cult of Ragnaros making a return to topple Moira as Queen of the Dark Irons and return it to the old Monarchy by trying to bring back Ragnaros and restarting the pact their former king made with the Firelord. (This is lead by High Justice Grimstone [that one dark iron dwarf we meet in the arena in Blackrock Depths that we never dealt with).
- The Scarlet Crusade returning in a larger force and occupying Fenris Isle, the Forsaken dealt with some of them, but the rest escaped including two named high-ranking officials named Crusader Alrick (Champion of the Scarlet Crusade), Inquisitor Fairbell, and Huntmaster Scarborgh. All three of these named NPCs may be replacements to other familiar named NPCs in the Scarlet Monastery like High Inquisitor Whitemane, Renault Mograine (his successor Commander Durand in the MoP version), and Houndmaster Loksey (Houndmaster Braun in MoP).
--[The interesting thing is that the Scarlet's were using Fenris Isle as their base of operation against the Forsaken, but before that.. that island was under the Bloodfang Pack's jurisdiction in BFA and it was re-affirmed in the Exploring Azeroth: Eastern Kingdoms book.]- Similarly, Southshore was retaken by the Alliance (via BFA Mission Table) and is undergoing the clean up and restoration (according to Shaw's notes in Exploring Azeroth)
- When the Scourge went rampant, they attacked Lakeshire in great numbers. It's unknown how much damage was done, but several people including the Blacksmith, did die when the Scourge attacked.
- When we recruited the Mag'har Orcs, we didn't just bring only them with us... We brought other races like Ogres, Gronn, Goren, Saberon, and Botani. The Gronn and Ogres stayed with the Mag'har while the Goren fled to Durotar while the Saberon and Botani fled to Northern Barrens.
- In the Orc heritage armor quest, the player meets with the Spirit of Thunder Ridge, Owa'nohe, to aid her and receive a blessing of the land. Gathering seeds from the flooded ridge and planting them near Owa'nohe's remains.. This will allow Thunder Ridge to grow trees and the Thunder Lizards will return to the land again.
This is only the newly added stuff. There's also the Mission Table Quests from BFA in relation to the achievement known as Azeroth At War which detail a list of different quests from Kalimdor to Eastern Kingdoms, establishing which areas the Horde and Alliance are occupying. I'm not gonna list all of them because the current list is big enough as it is and having to look through the other unfinished plots from Cata is going to take a while to check each one... but the most prominent one being Bael Modan in the Southern Barrens.
The only one I'm unsure about is that the Human Heritage Armor quest resolved the issues that the Defias had and we probably won't be seeing the Defias again. Though, it does point out the corruption behind the Stormwind Nobility and that there's a chance they might mess everything up depending on how deep the corruption is.