Sorry if this has since become wildly off topic! I only just finished with it.
Here are my quick ideas for zone groupings and concepts. Forgive me for how terrible the images are, I'm on my phone and don't have anything better to work with right now.
Kalimdor
Draenei Isles, not sure what name to give them. New Argus? Draemyst Isles? Zones would involve draenei racial storylines same as they do now, but modern and involving the addition of the Lightforged and former Manari. Minor horde experience involving mag'har orcs not trusting the draenei and struggling with their desire to attack, especially now that the manari have arrived as well. Some regular orc sympathizers who are iffy about the manari.
Hyjal Mountains. Heavy druid theme around Mount Hyjal. Moon Glade is part of this zone but serves the same purpose it does now unless Blizz is wonderful enough to actually add more class storylines in which cause it will contain druid quests. I forget too much about the story of Winterspring to say what should have happened here since to tie it to anything else but I'm sure there's a way.
Ashenvale Forest. The night elven lands forests that lie at the base of Mount Hyjal. Night elven racial story focus here involving borderline skirmishes with the orcs, but nothing that would escalate to bring the factions themselves into war. Lots of rebuilding, replanting, and cleansing the last remnants of the Legion's presence and damage.
Greater Durotar. Turning Azshara into their bread basket and containing the goblin pollution to their island. Maybe a storyline where a group of goblin shamans half-assedly are the go betweens for the industrial city of the goblins and the environmentalist orc shamans who are helping the orcs establish fertile farmland. Settlements of orcs near the Ashenvale Forest border who still hate the nelves but only ever have skirmishes like mentioned in the Ashenvale description. Lots of orcist racial focus in the Durotar area for new orcs to establish their identity.
Shu'halo Range. Tauren racial stories. Conflicts with centaur some Tauren make an effort to make peace with some friendlier groups of their ancient enemy. Grimtotem shenanigans and sabotage abound. Give the Grimtotem an established home area in the Feralas subzone to be based out of.
Unsure of name for Un'Goro, Thousand Needles, Dustwallow, and Southern Barrens. Botani and Saberon firmly established, clashing with the ogres in the Dustwallow area as both encroach on this territory the ogres have taken over since Theramore's destruction. Orcs to the north and Tauren to the northwest are working to keep the untamed wilds from the Botani stronghold of the former Wailing Caverns from seeping into their lands. Saberon have taken up residence in the now drained crags of Thousand Needles and the goblins and gnomes of the salt flats are struggling to run their business with such dangerous enemies nearby. Raceway is back and includes actual races and lots of mini games similar to the Darkmoon Fair, but in a casino environment. Main theme tying it all together is the invasion of the Saberon and Botani, the latter of which really want to get into Un'Goro.
Southern Sands. Qiraji forces have run rampant since Silithus was stabbed and are spreading across Uldum. Lots of bronze dragon clashes with the Infinites in the Caverns of Time. Air elemental politics and titan stuff in Uldum that reflects all the changes since Cata. Big underlying void issues with C'thun and cultists across the entire megazone.
Eastern Kingdoms
Quel'Thalas. Updated for everything we know about the blood elves since TBC ended. Silvermoon is rebuilt, the Dead Scar has been healed almost all the way down to Deatholme which is so cursed they haven't been able to fix it yet and negative spirits still manifest from here. Amani territory causing issues as the elves have promised the Zandalari they will respect the current Amani borders, but the Amani are not happy about these borders and are testing the commitment the elves made and the patience of the elves to respect them. Political conflicts among the elves who feel the magic side of their society has been too influenced by light zealots devoted to the new Sunwell. They are working on a way to restore the arcane nature of the Well and are getting too chummy with exiled void elves to make it happen as the void elves want it flipped back to arcane so they can be allowed to return to the Sunwell without risking it going void.
New Lordaeron. Forsaken have tentatively allowed human settlements into the former Western Plaguelands, with Anderhol having a small human population now, but not many are willing to live so close to the forsaken and are trying to encourage more humans to move in and basically gentrify the forsaken out of the city though political efforts. Scourge updates since Shadowlands and the efforts of the Argents. Lots of forsaken identity focus and the many different subgroups vying for more political influence. Unresolved tensions along the border with Gilneas but nothing that would cause a faction war. Scarlet Crusade plotlines that relate to next zone as well.
Not sure what to name Gilneas across to Hinterlands. Dalaran is stationed in its crater but is still considered to be a mobile city. Mage related focus in this area. Alterac Mountains includes thr Valley and has a proper Frostwolf presence as they begrudgingly allow dwarves to research the area under the supervision of Frostwolves and Reliquary members. Quests based around the history and artifacts the dwarves have uncovered and the conflict between them and the Frostwolves as they push to be allowed to be more aggressive and expansive in their efforts. Gilneas obviously has worgen racial focus in that subzone, and humans who want to live in New Lordaeron but still don't like the forsaken have taken up residence in areas like South Shore and Stromgard where there are secret illegal plots between some of them and some gilneans to seize New Lordaeron and exterminate the forsaken, backing Scarlet members who have infiltrated the settlements to spread their message and recruit more followers.
Khaz Modan. Ironforge focus with lots of Wildhammer integration in the Twilight Highlands. Cleansing of Grim Batol with the help of void elves. Aerie Peak still exists in previous zone but many Wildhammer are attempting to restore Grim Batol to its former glory so the majority of actual Wildhammer story takes place here. Dark Irons have a little presence around Ironforge but this leads to the Cult of Ragnaros plotline in the next zone and most stories here involve the Ironforge dwarves. Dam is fixed.
Shadowforge Ridge. Territory of the Dark Irons and storylines involving the Cult of Ragnaros. Small issue with remaining Black Rock Orcs who still wish to occupy the area and have managed to ally with some assholish but not corrupted black dragons who feel they should still have claim to the mountain. After being overrun by Scourge, the Redridge Mountains are abandoned by humans and have been taken over by gnolls and decay magic. The Dark Iron wish to get rid of the gnolls so they can have the fertile and unscorched lands remaining from the original Redridge Mountains they currently occupy, wishing to rename it all to Dark Iron Mountains (or the Dwarven equivalent). Shadowforge City is an uninstanced location and quest area as well as a dungeon or raid. Tensions between the Dark Irons and Stormwind as the Stormwind nobles do not want to give up the territory despite it being abandoned, with Moira guiding her son through the diplomacy of dealing with the issue.
Stormwind. Human racial storylines involving the nobles, Westfall farms, spooky stuff and Worgen rebels/exiles hiding amongst the feral population and rallying them to try to take over to build an army capable of marching North to exterminate the forsaken, who were reluctantly exiled by Greymane for threatening the peace between the factions. Some Stormwind nobles are secretly funding their efforts. Vanessa and Defias issues. Deadwind Pass is in this zone but only has high-level enemies and should not be ventured into by newly leveling players, though they may be flown straight to Karazhan to meet with Khadgar for something.
Some name reflecting the jungle and swamp somehow, and the Gurubashi preferably, but I can't think of anything right now. From the jungles of Stranglethorn Vale up to the Swamp of Sorrows, both are expanding into the Blasted Lands and reducing the Blasted Lands portion. Zandalari trolls who practiced blood magic have made it off Zandalar with the help of some unruly Gurubashi and they have taken up residence in the swamps and jungles. The Darkspear have a big presence here and have taken Zul Gurub for themselves as a capital (though they still have the Echo Isles as the Kalimdor outpost). There is a guerilla warfare issue with not knowing who are the allies and who are enemies, as the blood trolls aren't outwardly corrupted and crazy looking while living among the regular Gurubashi trolls who are neutral with the Darkspear tribe. There are of course pockets of outward blood magic and Hakkar worship, as more and more surviving Nazmir blood trolls arrive, smuggled in by secret blood magic using Zandalaris, and settle in the swamp, drawn by Hakkar now that G'huun is gone. Darkspear are trying to keep the peace with the neutral Gurubashi and Zandalari while trying to flush out the blood magic users and having difficulty telling who is who. Maybe Sunken Temple raid or something.
PHEW that took forever to write off and on for hours. I probably shouldn't have gotten carried away detailing what the storylines could be and just stuck with saying "race storylines here". But that's the basics of some ideas I had for how it could work for each zone. Feel free to correct me on why some groupings or story focus ideas wouldn't work, if you can stand to read all that! There's obviously a ton more that can be done in each mega zones, but these are some examples for potential plotlines. There would obviously also be gnome stories in the appropriate areas, pockets of Pandaren settlements and culture, and so on.