These are some good ideas. A few of them might take some fine tuningOverall excellent post OP I agree with the other ones not quoted, would like to add a few more of my own:
1. Ingredients such as spices, apples, and Fresh Water once again required to cook certain recipes.
2. Classes dehomogenized, classes have distinct mechanical differences once more e.g. Druids will no longer have a ressurecting spell other than Rebirth.
3. Dungeons Wailing Caverns and Sunken Temple will be restored to their original size.
4. Mounts will no longer be able to be obtained until level 40 and level 60 for epic mounts.
5. Alchemy once again requires different types of vials for various potions.
6. Enchanting once again requires upgrading your enchanting rod to create higher level enchants.
7. New dungeons include some larger ones such as Blackrock Depths/Spire and Mauradon.
8. Guild levels and perks removed, removing the incentive to mass invite randoms for Cash Flow. IMO players should join a guild for the people in it and ease of communication/organization, not a list of passive buffs for being in one mechanically handicapping yourself if you'd rather play solo.
9. Lengthy attunement quests for raids reminiscent of the Onyxia's Lair chain.
10. Heirloom gear is removed, replaced with purchasable BoA enchantment scrolls that increase experience gained when below a certain level once attached to gear.
11. Profession specializations (such as tribal/elemental/dragonscale leatherworking) returned.
12. Reinforcements removed from Alterac Valley and Warsong Gulch.
13. Alterac Valley NPCs buffed, Korrak the Bloodrager and the Winterax trolls return to the Field of Strife.
14. Dungeon Finder removed, replaced with the Looking For Group interface from patch 3.1.0. LookingForGroup channel is only accessible when using the feature but is once again global.
15. LFR removed, replaced with the new Raid Browser. Raids have only two difficulty settings: One that starts at Flex(Normal in WoD) difficulty at the entrance and by the endboss is Normal(Heroic in WoD) difficulty, and a second that starts at Normal(Heroic) difficulty and by the endboss is Heroic(Mythic) difficulty.
16. Number of flight points reduced.
17. Portal to Pandaria in SW/Org removed, you now take a Zeppelin or Boat route to get there (like Northrend).
18. Portals to old cities in Shattrath/Dalaran/Shrine removed, portals in cities to the Dark Portal in Blasted Lands and to Cata zones except for Deephome removed.
19. Battlegrounds can once again only be queued for by talking to a Battlemaster.
20. Justice/Valor and Honor/Conquest points can be sent between characters on the same account.
21. Fishing once again requires fishing in areas of the correct level to gain experience.
22. Mining nodes, leather, and herbs take twice as long to gather.
23. During nighttime the world is much darker and ambient more how it was pre-BC.
24. Certain spells and spell upgrades are no longer taught by trainers and must once again be learned from a tome.
25. Buffs are returned to 30 minutes and group-wide buffs require reagents again. Paladin blessings once again last for only 5 minutes.