I've done some testing with a ProBox 4HD Enclosure which allows me to switch between USB3.0 and eSATA (3GB/s HDs). Sustained transferring of many large files (300GB+ move of well over 100+ HD video files), eSATA performs marginally quicker. On quick file pushes, eSATA transfers substantially quicker. I imagine the SATA to SATA connections help with this immediacy. You can also format stripped arrays with eSATA for even faster performance which I can't get to work over a USB3.
I've got (4) 2TB 7200RPM drives in the ProBox and was transferring from one of those drives to the other for this test. Sustained speed was about 69-65MB/s on eSATA...USB3 was around 63MB/sec
As for transferring from my native 3TB 7200RPM, 6GB/s HD on my computer to a ProBox drive, eSATA was MUCH faster. Same sustained speeds for USB3 as before, but I averaged about 90MB/s, sometimes peaking @ 120MB/s, albeit briefly.
I am running the latest drivers and BIOS on this PC which I built about a month ago, so old USB3 drivers/BIOS is not an issue for me.
USB3.0 wins for convenience, eSATA for performance in my book.
PC Workstation Spec:
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ASUS P8Z68 DLX Motherboard
i7-2600K 3.40GHz Overclocked to 4.5GHz Turboboost
ASUS GTX570 1280MB GDDR5
16GB Corsair Ram
120GB OCZ3 SSD - Win7 Pro installed
(2) 3TB, 7200RPM, 6GB/s file storage drives
ProBox external drive encloser - (4) 2TB, 7200RPM, 3GB/s file store drives...eSATA or USB3.0 interface