One thing is the theorical speed an USB port (or whatever port) protocol can give and a quite different thing is what actual speed a device can give. Many flash drives and mechanical drives cannot reach those max transfer speeds. True bottlenecks. It often happens if you don't thoroughly check the specs when buying devices. They can use a given protocol, let's say USB 3 or SATA... but doesn't imply that they're able (designed or optimized) to use the full available bandwidth. Some flash drives or hard drives are faster/slower than others. Just check the specs.
A typical example. Theorically, USB 2.0 is faster than Firewire 400. But in the real life, most USB 2.0 devices give much slower transfers than most Firewire 400 devices. Normally devices implemented with FW400 are intended for high data transfer usages (Soundcards, etc...). While USB 2.0... well, just for plain data transfer in so many cases. Far from optimized and intended to be as fast as the protocol allows. The transfer speed is set by the slowest link of the chain (Device-cable-HUB). If a hard disk is slow itself, It doesn't matter how fast the transfer protocol can be.