I imagine that the Siege of Orgrimmar would be the suitable time to add cross-faction raids and dungeons to the game. (Rift had this feature since their last expansion this year already, so would only make sense that Blizzard at one point would do it as well.) In the Vol'jin and Baine cutscene they are after all talking about seeking out allies 'beyond the Horde' to take over Orgrimmar.
Basically it would let you make 25 or 10-man raids with a mix of Horde and Alliance, LFR will pool both Horde and Alliance together in the same raids, and LFD will also pool players from Horde and Alliance together.
Anyone want to take a bet this is gonna be the super secret grand feature in 5.4 that Ghostcrawler has been talking about?