I did a ton of research on this before making a decision. As others have said, opinions are all over the place and there's no "right" answer.
Bare Bottom-
Pros: Easy to clean, Cheaper, lower non-organics if skimming/changing filter media regularly
Cons: Looks unnatural (imo), critters that sift sand for food won't be happy, fish that like to burrow / move sand won't be happy, less bacteria growth
Shallow sand bed- .5-2 inches
Pros: looks more natural, crabs + stars + worms and the like will consume and break down larger organics more readily, fish feel more comfortable (imo...maybe not), suitable for some types of spawning rituals, more bacterial growth
Cons: fills up with organics, requires more thorough siphoning, more expensive, can scratch glass when cleaning with a magnet, potential for more algae growth
Deep sand bed- 4+ (this fad seems to be going away, but it is generally agreed that this is a longer term solution for larger systems where the sand bed will not regularly be disturbed)
Pros/Cons: Honestly there were too many / varied opinions on this. Some people say it's a ticking timebomb, and that if you disturb it or a power head falls it will nuke the tank. Others say that it creates a much more stable system with significantly higher biodiversity. It can lower nitrates if there is a large enough surface area for anxiolytic bacteria to grow - but you really need a big tank.
Nowadays there seems to be a consensus that a large remote DSB is the best usage.
In the end - go with what you want to look at day to day. If you have critters that require a DSB (sand sifting stars, some gobies, clams) then use one.