Although some USB 3 drives test somewhat faster on USB 2 ports - you still have only a USB 2.0 bus. Plugging in a USB 3 device does not, somehow, give you USB 3 speeds. The internal bus remains USB 2, and you can't change that with an external device.
But, then it would be nice to even have USB 2 speeds, for sure!
Perhaps there will be some improvement to file copy speeds if you erase the drive, and change it over to a Mac OS Extended format, using your Disk Utility.
Finally, if you are using NTFS drives, then you must have installed an NTFS driver. Perhaps the drop in performance is caused by the NTFS driver that you are using.
If it's the free NTFS-3G, then that's known to have poor performance, compared to full speed drivers, such as the commercial Tuxera NTFS driver.
http://www.macupdate.com/app/mac/33122/tuxera-ntfs
If you need to continue to have the drive formatted NTFS (because you need to share with Windows, for example), then the commercial NTFS driver may help, assuming you don't have that paid-for driver yet.