Well, bare bottom lets you be sure there is nothing built up on the bottom of the tank. You can see it and siphon it away immediately. No hassle setup and can be good for things like growing out fry.
Substrate looks nicer, gives a medium for planting, provides a more natural atmosphere in your tank. It is sometimes needed for breeding certain fish and some fish need something to dig in in order to be comfortable. It does collect debris and is more difficult to keep clean than bare bottom.
Sorry if all I said is just plain obvious but I couldn't think of any other thing you might be looking for in answer to that question.