Well I for one like the legacy of BIOS, esp given how clunky and down right poor the vast majority of motherboard OS software is I'm happy they are forced to deal with a very basic system.
As Abit proved with uGuru you can make some very good automated fan controls with it and for doing such a low level task as controlling fan speeds based off temp having the underlying hardware handle it at a very base level is a good thing and not having it running crap in the background of the OS chewing up cpu cycles and memory.
One intresting trend is the loss of PWM fan headers, not that long ago we where seeing more than just the cpu fan being the only PWM header on a board and it looked like a full set of fully conrtolled PWM fans would be the way it went, but now it's just the cpu.
it would be really nice if a motherboard manufacture got together with some one like zalman or aerocool and fully intergrated a hardware fan controller into the motherboards.