Wait a sec guys....maybe I'm missing something really basic about physics, but...
If you have a bigger drive you have bigger platters. The relative speed increases as you go outward, which is why we see drives having their highest transfer rate on the outer tracks. Assuming you had the same hub size a larger platter would give an even bigger different from inner to outer tracks, but the outer tracks on a 5.25" drive even at a low rotation speed (say 5000 rpm range) would be better than that of 3.5" drives at 7200rpm. With some smart partitioning utility that allowed you to set the outer tracks as C: System and inner as D: MP3&PR0N a low rpm 5.25" drive could achieve both high transfer rates and, assuming same platter density, huge capacity. Or same capacity with fewer platters, which have to be more expensive to manufacture than the cast aluminum case that makes up the HD body.
Seek times wouldn't benefit though, so while you could have a low rpm/high transfer rate drive it's seeks would be poor. In the end that, along with consumer expectation of 3.5" HDs because of their universal installation ability regardless of case would seem to me to be the primary factors. Transfer rate wouldn't, again, unless I'm missing something.