Well, Yamato isn't the Devil Arm Sparda used the most. I mean look at Dante, all these devil arms and he still uses Rebellion. My point is that Yamato was given to Vergil and has a deeper connection to him rather than Sparda. Also I've never really gotten the reason for Sparda returning since he saved the world, fell in love with a human and had two kids with her. Whilst Vergil was defeated after failing to achieve Spardas power, then defeaten again and enslaved by Mundus. So I'd say that Vergils soul is probably restless and tries to finish what he started and thus he tries to come back.