Personally, I can't think of any reason not to use BizHawk for any of the platforms it supports, except for the odd rom hacks here and there that only work on less accurate emulators.
Because some people want accurate emulation and BizHawk is made for speedruns not for 100% accurate emulation.
I wonder why no hardware emulator for Nintendo 64 exists, might have to get one of those things to load roms into a N64.