Been following this thread for a while. I just did some drive testing on my MacBook Pro which as an Intel SSD as the main drive and a 500gb 5400rpm drive in the optical bay. I also tested my 500gb Seagate USB3 external drive, but my Mac's USB ports are only 2.0 so they were clearly the bottleneck in that test. Also my SSD is only able to run at SATA 2(3.0 gbps) speeds instead of SATA 3(6.0 gbps) speeds, but I'm not sure that this SSD is fast enough for that to make much of a difference.
Anyway here are the results:
Not sure if this helps anybody, but I thought it might. I know the USB3 external drive is much faster on a USB3 port as I've used it on my brothers newer laptop that has USB3.