For the average user, probably: I've never found a BIOS which is as rich and flexible as SpeedFan is.
I agree completely into speedfan being much more customizable, but at the same time for me never have worked perfect in terms of recognizing all sensor. For the average user, in my personal opinion, FanXpert2 is just very easy to setup and run, and its garantee that will work with the sensor the motherboard comes.
Now on pure bios, some manufactures are doing their homework, Asrock in haswell mobos is coming with 5 breakpoints and 5 temp thresholds, still small compared to 16 of speedfan, but i live with 2 on MSI Z87-GD65 and been great, i really like not having extra programs loaded on memory, even though i only use windows on my PCs, this is very practical for people running linux distros, or whatever other os.
What its missing is more PWM headers, its fine as PWM splitters makes working with PWM fan very easy and safe, but if more real PWM headers were included it will even give more control to the users.