That's because you have NO usb3 ports AT ALL. There is a huge difference. Usb2 is perfectly good for lots of stuff and I don't see a single reason to kill it. It's definitely much better than nothing. And the CPU can't provide enough bandwidth for an unlimited amount of USB3 ports, so it's quite wise to use that bandwidth more effectively and add some usb2 ports instead. In this specific case, there is only one usb3 port and a tb3 port, but I guess they chose usb2 because it's cheaper. Still, there's nothing wrong with it. You have your usb3, and you have your useless rounded port (unless eGPU is supported). What else do you need?
Oh, and don't forget another thing - USB 2.0 allows up to 60MB/s, which is near the top of a typical magnetic hard drive's speed. So, you know, USB3 will only make it like 10% faster.