I have to say I take any idea of Specialist games being handed to FFG with a massive pinch of salt. GW would not want to hand over miniatures based games, which all the specialist games are. Blood Bowl aside (which is a board game, just with miniatures as the pieces) they cannot be played without miniatures. However, I could see things like Warhammer Quest, Heroquest, or Space Crusade being handed onto FFG, as they are basically board games as well. However, I believe Warhammer Quest and Space Hulk were explicitly left out of the agreement (as GW thought they might want to do something with them in the future, like they did with Space Hulk in the end), and I imagine there might be some licensing issues with the games that were shared with MB.
Certainly they could have non-setting changing events, which is what the Medusa V campaign was. However, it was 1) a bit let down after the Storm of Chaos, and 2) they kind of blanded it out by not producing anything special for it and also making it a royal rumble for everyone. There wasn't really any plot of significance to it, particularly because of this (by narrowing it you can make it matter for those factions, like they did for Armageddon).