I'm new to fish keeping, but this is what I have experienced with bare bottom and gravel.
When I moved my 20 gal to my living room, I found all of the waste under the gravel like you mentioned. I had been doing weekly water changes with gravel vacuums, so I don't think that it was my lack of wc. I ended up lowering the gravel to as low as it would go, but could still hold plastic plants. This seemed to help a little. When I removed the gravel again to make the 20 a Q tank there wasn't as much of a mess.
The problem I have with bare bottom is that my filter on the 20 doesn't seem to have much mechanical filtration power. If I want the aquarium to be clean I have to take the waste out from the bottom with a brine shrimp net on a daily basis. I think it helps with seeing if your fish are eating or sick though.
Also another thing I've noticed is my albino bichir seems to have a harder time griping the bare bottom while moving around. My other bichir, which is on substrate, has no problem.