For me personally bare bottom has lots of advantages, but also disadvantages. After a while the bottom is not bare at all, because coraline algae will cover it. The main advantages is that a bare bottom have less place for detrius to collect, because you can direct your pumps exactly where you want and how strong you want, because there will be no sandstorm in your tank.
The negative thing to going bare bottom is that there are several species you may want to keep that will be needing substrate and without substrate it will be very difficult to keep them alive. Substrate is also the meduim that a lot of smaller life choose to live in , that is also beneficial in removing toxins and acting as a food source for reef inhabitants.
I've been running bare bottom for long time very succesful, but on my current tank, I decided to live with the extra sleb a substrate brings, because of the inhabitants I want to keep needs substrate.
So primarily , according to me, it is a personal choice as to where you want to go and what you want to achieve. That said, substrate make a tank look more natural.
