Hard drive performance is all about areal density and rotational latency, regardless of the form factor.
Take a 2.5" 100GB drive versus a 3.5" 200GB drive. The areal density is higher with the 3.5" drive and if both have the same rotational latency, then the 3.5" drive is faster.
Take a 2.5" 100GB drive rotating ay 15,000 RPM, versus a 3.5" 200GB drive rotating at 5400RPM, the and the 2.5" drive will be faster due to a significantly lower rotational latency.