Sand
Pros:
1. Much easier to clean as the wastes are lighter than sand.
2. Makes it easier for most fish and invertebrates to burrow around.
3. Friendly to fish with delicate barbels.
Cons:
1. If I change my mind on rescaping tanks, sand is a pain to remove.
2. Becomes compact easily and becomes potentially dangerous if it binds and forms anaerobic pockets. For this reason, you need to stir it or rely on your trumpet snails to do the job for you (though the MTS will not burrow too deeply).
3. Can damage powerheads if the powerheads are turned on while the sand has not settled completely yet.
Gravel
Pros:
1. Allows oxygen to penetrate through plant roots much better therefore, it is more suitable for planted setups.
2. Easier to remove if you change mind rescaping the tank.
3. Much easier to rinse around unlike sand before setting it up.
Cons:
1. Pain to vacuum around as the wastes are trapped.
2. Most fish choke on gravel easily although this rarely happens.
Bare Bottom
Pros:
1. Very easy to clean. If you have issues with poop, direct the powerhead carefully along the bottom to sweep them into the filter.
2. No anaerobic pockets or breeding bed for bacteria, virus and parasites to worry about.
3. Even if plants are placed in pots, maintenance remains easily done without the necessity to vacuum around.
Cons:
1. Unnatural or boring for some. Personal taste varies.
2. Cannot be used for planted setups unless you intend to keep the plants in pots instead.
3. Fish that need them especially loaches and other known burrowers/diggers will never be comfortable in this kind of setup.