the right substrate can be useful on multiple levels...it does provide some extra area for bacterial colonization, but more importantly for larger gars (and particular species), you can get substrate that buffers the pH fluctuations in the tank. crushed coral or aragonite sand works well to buffer the pH in an aquarium (particularly useful with larger gars, and also with Cuban gars at medium-large sizes).
the general trend of a tank is for the pH to drop due to waste products; then with water changes it's somewhat returned to a 'normal' state (neutral or a bit higher works best for gars, although some lower pH levels work as long as they don't fluctuate much...the fluctuation is the hard part to control, especially at low pH).
bare bottom can work as long as you can keep up with water changes (or do them more than needed to maintain consistent pH); but even gravel can help buffer the water a bit (depending on the material).--
--solomon
