Quite a few people do run bare bottomed tanks. I can't say how it would work with the pleco, as I have never kept one, but as for all the other fish I'd say it would be a good thing, just from what I have heard, not from any personal experience other than my hospital tank.
You can keep potted plants in a bare bottom tank. It would be much easier to clean, I believe.
How thick is your gravel? How are your nitrate readings? The reason I ask is I'm wondering if there's some reason your gravel is staying dirty enough to be giving you problems. Is overfeeding a possibility? Is the pleco producing too much waste? I usually vacuum about half my tank with each water change of 25-40% and it's not dirty enough to make me want to continue until the water is nearly gone, which it sounds as though that's what you are experiencing.