This is subjective. There are too many variables to consider when you think of the advantages and disadvantages of a barebottom setup. Unless you have fish that really like to dig around or that substrate is necessary for breeding purposes and natural behavioral process, then there is nothing wrong with doing a barebottom setup.
For example, quarantine and hospital tanks should always remain barebottom. The reason is very simple. It is for hygienic reasons. Most parasites make it harder for us to destroy them completely when they use the substrate to attach themselves thus any attempts to vacuum the eggs, juveniles and cysts would prove a rather futile effort. The organic wastes accummulating assuming we are using gravel which does trap organic wastes, makes it harder for us to maintain the toxic effects of the medicines used to destroy the parasites. Bear in mind, many chemicals degrade over time and have to be repeated in the process. This includes malachite green and trichlorfon, both of which are often used for parasites. Malachite green itself binds quickly on organic matter making it ineffective in the process. With a barebottom setup, no wastes will remain trapped in the tank for a long time which would quickly deteriorate the water quality thus stressing the fish more especially when they are isolated in hospital tank. Such scenario defeats the purpose of isolating the fish.
Right now, I keep goldfish and snails myself. Goldfish have no use for the substrate other than to keep foraging around it which they will still do with a barebottom setup so removing the gravel was not a total disappointment for me at all. I had to do it to make maintenance much easier for me. Goldfish excrete a lot of wastes and I had trouble trying to vacuum all the wastes around the tank. As for my snails, with the exception of the trumpets and assassin snails, others have no use for the substrate especially my apple snails. Considering I keep hundreds of apple snails, vacuuming their wastes was a terrible job for me. Their wastes disintegrate easily so I decided to keep two tanks barebottom for them. I could have done with the sand definitely but I would prefer a barebottom setup on this one so I can be assured the wastes are completely removed to prevent the water quality from deteriorating rapidly.
Hope this helps.