There have been lots of improvements in transfer rates in a number of areas. The issue with high data rates was that if you sent data too fast then the individual bits you sent down the line would interfere with each other and end up just a blur on the receiving end of the cable. Today we have a lot better knowledge of how this happens and what we can do to prevent it or interpret the blur so we get the data through. In addition we have found out what kind of cable works best and how to make it on the cheap. The issue was that USB did not use that cable or connector. So while other technologies like PCIe, SATA and HDMI were able to use the new technology as it came out USB was left behind. The USB 3.x standard was designed almost 10 years ago but it required new connectors, new cables and new controller chipsets. Thus it took some time to become common.
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