First off, in HDTune we can see the minimal difference between the two SATA standards.
Though the higher bandwidth does result in faster maximum reads, in overall real-world performance the advantage is just not that significant. Even worse, comparing the Seagate Barracuda XT 2TB on SATA 6Gb/s to the older standard on our Intel Core 2/Asus P5E3 test rig, SATA 3Gb/s consistently outperforms the newer and supposedly faster standard.
We're frankly at a loss to explain this reversal of what one would expect, since if anything the newer board with its more recent firmware should outperform its older cousin on the old SATA standard, let alone the new. The only possible conclusion to part of this puzzle is that the Intel 3Gb/s controller outperforms the Marvel 6Gb/s one regardless of bandwidth.