My argument would be that SNES9x has the objective of being as accurate as possible while still keeping the speed fast enough to permit portability to a wide variety of platforms.
BSNES won't run well on lower-end hardware. At all. byuu has stated that he can probably do more optimization, and he will probably continue to do so, but his first step was to get the emulation as accurate as possible.
It's entirely possible that BSNES and SNES9x will converge to a point where there is next to no difference between the two emulation-wise, but they're approaching that point from two different directions. BSNES started with accuracy first and foremost; SNES9x started with playability and 'apparent' accuracy. BSNES doesn't need any sort of timing hacks. That's not the case with SNES9x - yet. They've managed to trim out a lot of them as their accuracy increased (in part thanks to byuu's kind assistance).
The other point to make in regards to BSNES is that it doesn't have a lot of usability features - extensive support for different formats, movie recording, et cetera. byuu used to do that, then he got to the point where he was doing more work on the front end than the back end. Now he leaves that bit to other people. (Like the SNES9x team!