Rock is fine. The pro is the look that you are speaking of. Another small pro is increased surface area for beneficial bacteria to attach. The cons, however, are the maintenance. With rock, it becomes more difficult to scoop/vaccuum out debris and muck. The muck and debris will collect in the rocks and the housekeeping of those rocks then becomes troublesome. You end up either scooping rocks out in your nets or being unable to get the pond as clean as you would like. My vote would be to forget about the rock and grow more plants to camoflauge your shelf....but to each his own!

Use large flat rocks on the shelf,(you can also mix in some round rocks) plant your plants in pots between the rocks hiding the pots...you can also plant many things bare root between the rocks. It will give your pond a very natural look.
Avoid the small rocks and pebbles, hard to keep clean the they get knocked all over the place.
How deep is the shelf? We are talking about a shelf in the water right?

Joann

I put some river rock on my shelf (need to finish this) & the fish love it. It's barely one thin layer, you can still see the liner through it but the fish are always sifting through them. They really seem to like the rock. Also I've noticed that's where the tadpoles & the baby fish hide, they go under & in between the rocks.

Not a rock fan unless large and easy to clean around them.

I have large flat flagstones on the upper part of my large pond, which has a shelf about three feet wide and the water is from six inches to twelve inches deep over this area.
It does become covered with silt and algae, which I clean off with a deck brush every so often in the early part of the season and use a sharp spray head on the garden hose to blast out the gunk that gathers in between the stones.

I net out the algae and larger bits of debris. The smaller particles and silt goes out through the pond's bottom drain into the sump.

Over time the plants cover over most of the surface of the flagstone, so this keep the area algae free and clean.

I like to see the flagstone clean so I don't mind the extra work of keeping it that way.
If you do not clean it you may as well not bother having flagstone there, as it will be covered with algae and pond gunk, just like the liner is after a short period of time.
As far as having river rocks on the bottom or even covering the shelves, personally I would stay away from that, as they would be difficult to keep clean and even more difficult to get the gunk out from between or under them.
"Horton"

We've just recently removed the river rock from our pond bottom. Yes, I do think the koi enjoyed it and it did seem to keep their attention away from uprooting our plants. But the muck that accumulated on the rocks was ugly and way too much work! No more rock for us.

I left mine on the upper two tiers b/c I plant my lilies directly in them. I removed them from the bottom of the pond. A maintenance nightmare!

I also tried the rock despite what I read on these sites. I used rock about two inches big and it got so dirty so fast, it looked disgusting. The next year I took it all out. The disgust I found under the rock was awful. I had to empty the whole pond and just clean the whole thing out. I loved the look for the first 3-4 days before it was covered with algae. I would occasionally try to spray the rock off, but too much trouble. Hmmmm, flagstone on the shelves. Sounds interesting. Here we go again.

THANKS for the replies....I figured it might be a maintenance nightmare. I think I'll just stick with trying to cover a majority of the surface with water plants.