Two things that came to my mind:
Shanks waited for Ex-Rocks pirates to be eliminated until he started to go after One Piece
Blackbeard wants to be king of the world, something Xebec tried to do. Shanks vs Blackbeard was heavily hinted at Marineford.
If Figarland were the enemies of Rocks, and if Rocks destroyed Shanks homeland then this can give us some hints about his motivation. But what could it be? Does he try to protect Imu? What are his plans for the new era? Is he good, bad or something in-between?
I can see him having a huge antipathy for Rocks pirates and his "successor" Blackbeard. Maybe he is siding with the government to fight a bigger threat, just like Roger fought with the marines to protect the CDs. This is why he talked to the gorosei. That threat must be Blackbeard.