There are a couple of things at play -- one is large data, one is small data. Large data files take time to transfer because of their size and a limitation of the bandwidth to write; this is why USB3 transfers faster than USB2. With small files, you are writing the in/out and the tiny amount of data - it's fast, but the operating system / file system limitations make this a slow process. This is why writing 10 small files can taking up a tiny amount of space can possibly take longer than 1 large file occupying more than those 10 files.
Want to know the true speed of your device? Try using a speedtest which is capable of writing both large and small files and test the read/write speeds of both filesizes. Not all devices are created equal - a USB3 chipset could be junk and perform slower than a USB2 device!