I have done bare bottom in the past and decided to go back to sand because for me, keeping it clean was more work. It depends on how you want the bottom to look. It's much easier to clean detritus on the bottom, just suck it out, but on the other hand, there is nothing at all to hide it so it shows very quickly. If you go BB, are you going to let coralline grow on the bottom? If not, it is like having a whole other window to keep clean (that you can't use a magnet on). But if you don't mind sucking out detritus a couple times a week and don't want the build-up of organics in the sand, go for it.
As you mentioned, it rules out sand dwelling animals when you are already limited by tank size. I do love my goby/pistol pair...