With the latest revelations about Ace, I think Shanks wanted to stop THIS from happening. He knew that Blackbeard was someone that Ace would not be able to capture/defeat, and that the result would be this. That's why before their fight, Shanks mentioned to Blackbeard about his 3 scars, and how he had received them before Blackbeard even had a devils fruit. It was obviously Shanks talking up Blackbeard's fighting ability.