Why is my external hard drive transferring so slowly on USB 3.0?

USB3 is not going to be able to make up for a cheap and awful 2.5" HDD.

Those drives were pretty bad at the best of times and could probably manage 60-100MB/s at peak on a single solid transfer, for random seeks on small files they will literally drop down to single digit MB/s rates.

Have a look at the images for Seagate Backup drives at Anandtech. Note that these are for supposed "good" drives. When you get down to millions of tiny 4K reads the drive will spend a massive amount of time seeking, reading, seeking again, reading, maybe writing, and seeking a few more times for good measure. When copying tiny files the area you care about is looking at the "4K" section of CrystalDiskMark:

Which looks just awful. On top of the bad performance of the drive you are copying to, you may well have to contend with whatever performance you get from your source drive as well. If you are copying millions of tiny files from a 2.5" HDD to another 2.5" HDD then quite honestly you would have to have the patience of a saint.

If you create a single solid file using your favourite zipping tool and then copy that to the drive then you may well see the true transfer speed the drive is capable of.