i think it depends on the size of your tank and how much time you really want to spend cleaning it.
i use to have gravel in my 240gallon but i took it all out cuz it was a pain in the ass to vaccum the whole tank. i use to spend 4 hours vaccumming that bad boy and with a bare bottom i spend 30 minutes.
as far as beneficial bacteria, should'nt there be beneficial bacteria in the water anyway? i only see gravel as having a very small percent for harboring bacteria. as long as your tank is cycled, and you have a badass filter (i have a wet/dry), i don't think you need gravel. it's just all for the looks to me.