Most mobos fitted with an IDT IDE controller will support it - and what is there to setup? None of the three mobos I have that support IDT have any choices in the BIOS and none have any trouble running two drives at different speeds.
One drive per ribbon may theoretically be ideal but most people need more than two IDE channels and adding another controller (as I have in one machine where I needed five channels) seems a bit of overkill for the average punter.
As you say, SATA is now becoming mainstream, but I can't afford to change my main 160GB IDE drive in the excellent K7N2 Delta-ILSR for a serial one.....
Gotta agree that very few PCs are set up properly - it's rare to find one where a bit of tweaking and rearranging won't speed things up significantly (at least on the benchmarks).