I ran my 40 bare-bottomed for a while for reasons like cleaning ease but after I put a layer of fine gravel in it (light colored, no less) I would never go bare again.
It just looks so much better.
Reef tanks or those that are heavily planted are a different story. But for the average tank where the focus is on the fish, gravel or sand is a definite plus. And as for the poo factor, I have a large syringe with a 1/8 inch tube on it and a stiff wire (stainless) that I use to pick up the large morsels. A weekly vacuuming gets the smaller tidbits.