According to Ryan Payton of Kojima Productions, the new DualShock 3 controller will be more advanced than its predecessor.
During an episode of Kojima's podcast, Payton claims that the new controller has a better rumble function, adding: "I mean, it feels better." The biggest and most notable feature is the positional rumble technology, allowing for a more realistic feeling.
Payton also mentioned that the developers were given the tools for the DualShock 3 only weeks before TGS. It will be interesting to see what developers can do with the rumble after they have had more time with the controllers. Make sure to check back for more details.