The 5D and 5D Mark II share one other notable AF hardware similarity: both utilize a dedicated 32-bit RISC microprocessor to perform AF calculations (in contrast, Canon's Mark III models utilize DIGIC III for this).
This should mean the speed of autofocus will feel about the same as before, with one caveat: because the 5D Mark II's main CPU, DIGIC 4, is much faster than DIGIC II in the 5D, certain functions of the new model may end up enjoying a slight speed boost, even if they don't directly depend on the DIGIC processor to perform their specific function. Autofocus speed could well be one such function that is improved in this way, though whether any speed jump is noticeable or leads to a higher percentage of in-focus pictures is impossible to say without actually using the camera.
The 5D Mark II does include two more obvious changes in its AF system, relative to the 5D: it now has the ability to detect scene colour temperature and light flicker, then incorporate that as part of the camera's autotofocus calculation, plus AF Microadjustment, to compensate for focus calibration error in the camera body or combination of body and attached lens, has been added.