I've actually noticed that my HDDs in a SATA III will run closer to its listed theoretical read/write, SATA II would give me 1/2 SATA III speeds, and SATA I will give me 1/4th SATA III speeds.
For example, I'll copy/paste a 2GB file on my 3TB WD Black, and I'll get roughly
SATA III 120MB/s
SATA II 60MB/s
SATA I 30MB/s
for the same file.
It could be something else causing the slowdown, but I've always suspected the change in bandwidth between each SATA revision caused the changes in read/write.