Here are the changes occuring to the cities of both Factions:
Stormwind: Park District is destroyed. Stormwind Lake and Stormwind City Cemetery are added to the City grounds. SW Keep is being updated and is now much more regal. Screenshots can be seen here. Stormwind City
Ironforge: Possible entrance to the Hall of Thanes, as that is where the now petrified King Magni is. Ironforge is now ruled by the council of the Three Hammers. Moira Thaurissan, (brainwashed princess of Ironforge who has borne the late Emperor Thaurissan a son who is heir to BOTH Dark Iron and Ironforge Thrones), Muradin and Falstad Wildhammer rule Ironforge as a council with no official leader. Mekkatorque probably will be moved to gnomeregan starting zone.
Darnassus: Only changes here; there will be a Worgen District here and Rut' theran Village is separated from Teldrassil. It is possible due to Fandral Staghelm's incapacitation that a leader change might occur. [ See the book, Stormrage ]
Exodar: Probable Portal to Stormwind. Also Valaar's berth has a boat straight to SW.
Greymane City: It is both a city and a battleground in Cataclysm. Whether or not it will function as a true capital for the Worgen is as yet unknown. It has four districts and a large cathedral.
Gnomeregan: Only the surface will be retaken. Only acts as a starting zone. It may have a Flightmaster or some form of fast travel. Mekkatorque will probably relocate here.
Orgrimmar: Rebuilt after Deathwing's attack. Valley of Wisdom is now a Tauren District. Due to tension between Vol'jin and Garrosh Trolls have left Orgrimmar and are now n the reclaimed Echo Isles. Goblin slums will be added. The Leader's keep will be moved right into the valley of strength. (easier time for the alliance to run right in and either get maimed or destroy Garrosh.) Screenshots can be seen here Orgrimmar
Thunder Bluff: Will likely be empty of all Grimtotem. Baine Bloodhoof is now leader of the Tauren after Cairne's Murder, (the Grimtotems poisoned him.)
Undercity:Surface revamped for Flying mounts, looks awesome. Large force of Orcs have replaced abominations and Varimathras. After the Wrathgate the horde had locked down on the forsaken. Val'kyr may appear in the city after they join the Forsaken. Not much else is known at the moment.
Silvermoon City: Absolutely nothing as of now. However, Lor' Themar gets a model update! (Or just new gear..)
Darkspear Isles: Reclaimed Echo Isles, screenshots have shown it to be huge and much more inhabited. Will likely have a flightmaster and few other capital functions. Screenshots can be seen here. Darkspear Isles
Bilgewater Harbor: New Goblin Capital built on a large island in the middle of Bay of Storms. It;s got a large cannon on the peak. This will be the Goblin City. Will probably have flightmaster and possibly more capital city functions than Greymane City as it is NOT being laid siege to. Screenshots can be seen here.Bilgewater Harbor