Ducati don't want him to leave as losing 2 top riders in 3 years (Stoner + Rossi) makes them look bad and is bad for sponsorship, and Yamaha may not actually want Rossi himself when they could potentially get Dovi for less money. Rossi does bring strong marketing and sponsors however, which they may struggle to find if they chose Dovi, however Rossi won't be in MotoGP forever and teams need to start finding their own sponsors.
However, at Valencia Carmelo Ezpeleta said “I’m calm. Valentino next year will be on competitive bike, but I can’t tell you which. It’s too early to talk about it, but in 2013 we’ll see Rossi fighting again for wins“. This may be more political than Rossi or the teams themselves actually want.
With Stoner retiring, MotoGP needs another strong rider up front to keep things interesting. While Rossi's clock is ticking at Ducati, the Dorna clock is ticking for MotoGP to get viewers, sponsorship money and more bikes on the grid.
I don't think Rossi's move is good for Ducati (if they can make the bike competitive) or Yamaha (who could have Cal or Dovi) - but it is for MotoGP / Dorna.
I hope Volkswagen AG / Audi can bring some real world engineering in to Ducati and make it competitive for 2013. VAG also own 19.9% of Suzuki Motor Corporation which is another manufacturer I look forward to seeing on the grid. As much as I like Yamaha and Honda, it's getting a bit dull with only 2 manufacturers guaranteed places on the podium each race.