The system will use a "wired or wireless communication link," which may suggest at both PS2 and PS3 controllers being compatible with this feature. In addition, "the portable processing unit can be configured to provide additional functions, features, or enhanced operation when coupled to the control docking unit." It looks like players will finally be able to use dual analog controls in-game. (Note: hackers have already been able to do something similar.)
Of course, not all patent applications come to fruition in the marketplace. Regardless, this is certainly an interesting development, one we wouldn't mind seeing Sony pursue.