There actually is a good reason for the offset sticks:
The upper position, where the left stick and face buttons are on the 360 controller, is more comfortable to rest your hand on, so really both sticks should be up there if that was all you're using. However, it's easier to make a precision move when going from the lower position to the upper position than vice-versa (i.e. taking your thumb off the right stick to hit a button). Because you need to be able to quickly take your thumb off the stick to make precise button hits, but not the other way around, the face buttons need to be above the stick so you can make that type of move quickly and reliably. On the left side, however, that's not as much of a consideration, so the stick can be in the upper position where it's more comfortable to rest your thumb.