Simply saying that 2.5” drives are better than 3.5” models would be oversimplifying. The 2.5” form factor is not superior in all aspects, and differences such as data density and spindle speed also require consideration. In short, though, 3.5” hard drives at 7,200 RPM will remain important for high-capacity applications while 2.5” models will fuel mainstream servers for years to come. SSDs are increasingly important, but mainly in top-performance environments and as a replacement for 15,000 RPM drives.
Without question, the highest spindle speeds and state of the art technology determine throughput performance. However, I/O performance is mostly restricted by the physical performance of the read/write heads. Since these can’t be accelerated indefinitely, there are natural limits to I/O performance. The platter diameter of 3.5” and 2.5” enterprise drives remains constant, which means that I/O performance doesn’t change much. In our testing, the 3.5”, 15K RPM Fujitsu drive is only faster than the 2.5” 10K RPM Toshiba model because it spins faster and introduces less rotational latency.
A quick word on the interface: the choice of SAS 6 Gb/s or 3 Gb/s may matter for connections between JBODs and backplanes to the controller or host adapter, but it won't be significant for individual drives.
Translated into enterprise environments, it's easy to see that you can typically fit twice the amount of 2.5” drives into the rack space required by 3.5” drives. Blades don’t even support 3.5” drives because of their physical dimensions. Since capacities and I/O performance are almost identical between 3.5” and 2.5” products, but power consumption and dimensions are much decreased on 2.5”, the latter effectivly doubles power efficiency and storage density when performance per watt or capacity per space are concerned.