NO mechanical (spinning disk) HDD achieves a data transfer rate anywhere near 6 Gb/s. That is the max communication rate for the latest SATA versions, but the HDD itself is much slower. The best SATA mechanical HDD's can get to 150 to 180 MB/s (1.5 to 1.8 Gb/s) as an average sustained data transfer rate, but most new ones are closer to 100 to 125 MB/s, and older SATA units are slower. While these are faster than the fastest IDE units at 133 MB/s max (and probably slower than that average sustained transfer rate), the difference is not nearly as huge as you fear.
Aside from the speed rating of the HDD, what is the capability of the IDE controller on your old mobo? If, for example, it is rated at ATA100, no HDD attached will perform faster than that. And don't forget that you should be using 80-condictor ribbon cables from mobo port to HDD, not the very old 40-wire cables.