A bare bottom, or one covered with a fairly thin layer of finer substrate (sand) simply makes the debris more visible, as others have stated. This makes it easier to either siphon the junk out, or for strategically placed pump outlets and powerheads to sweep it towards the filter intake. I think one of the biggest problems occurs for folks who choose a coarser gravel; it's common to see pics of tanks with a thick layer of some coarse, angular gravel that is a perfect trap for uneaten food and other waste. Once this stuff falls into the crevices between the gravel particles, it ain't going anywhere.
Personally, I haven't "gravel-vacuumed" anything in a long, long time. I have sand substrates, just because I don't like bare bottom tanks and am a firm believer in the added surface area provided by sand for bacterial growth; I adjust the water flow to allow the filter to remove the junk for me; and, probably just as important, I have fish that like to stir up the bottom layer (Geos, etc.). Plants are either kept in pots, floating freely or attached to driftwood.