The way to think about drive speed is Bottleneck Analysis. As long as the connection methods are faster than the Drives, there will be no appreciable slowdown.
All single rotating and SSD drives available today and most Arrays are MUCH slower than SATA-2, PCIe, or ThunderBolt, so there will be no real-world slowdown.
"A chain is only as strong as its WEAKEST Link", and a drive is only as fast as its SLOWEST connection. In this case, that is the speed at which the data spins under the read heads, or the access time of an SSD. At this writing, these are all quite a bit slower than the Busses available. So there will be no real-world difference in where you attach those drives.
RE: SATA Bus speed:
SATA 3 is rated at 6G bits/sec, which theoretically is about 750 Mega Bytes/sec
SATA 2 is rated at 3G bits/sec, which is theoretically about 375 Mega Bytes/sec
SATA 1 is rated at 1.5G bits/sec, which is theoretically about 187.5 Meg Bytes/sec
Rotating drives available today, whatever their SATA spec, can source data off the spinning platters no faster than about 125MBytes/sec.
None of the SATA Busses is a bottleneck for consumer Rotating drives you can buy today. Trying to speed up the SATA Bus will not provide any real-world performance increases for Rotating Drives.
Even MOST common SSD drives are not bottlenecked by SATA 2.
>> If you have a faster SSD Data drive, consider mounting it on a PCIe card that features SATA-3 slots, but it may not be bootable from there.
There are no superfast PCIe-direct devices available today (except inside Apple computers), but rumors suggest we may see some in 2014.
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