To be honest, I think plug n pray is flawed. When it does work then it's great, when it doesn't then you'll get driven mad.
I've seem systems where the BIOS wants it one way and Windows wants it another. And you get stuck in an endless reboot cycle as each reconfigures it and restarts. Each one thought it was being intelligent and configuring the card properly.
In the end we had to force Windows to use the BIOS settings. Even though the PNP OS option was turned on in the BIOS which should have made the BIOS ignore it all and let the OS configure it, it kept doing something mystical to the PCI registers.
The "new" method now is ACPI which is even more useless. It relies on you embedding a chunk of interpreted code into the BIOS and having a huge bloated ACPI interpreter run it. In theory this would allow you to configure the device using anything that supported ACPI. However, the manufacturers still think the whole world runs Windows because they hack together something so that it'll boot up in Windows and then declare it done even if it's still buggy as hell.
Give me back dipswitches!