I think this is where we can fully agree.
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But this is were we disagree.
A gravel (or rock) bottom pond can be managed, but it's certainly not integral to well balanced pond. I've seen too many rock bottom ponds being cleaned out to think for minute that the stuff that accumulates in their is somehow beneficial to the health of the pond.
I accept that initially, in a new pond, gravel and rock in the bottom of a pond will have a neutral effect. What's more after a few months or a year the rock and gravel may have a beneficial effect due to the surface area and the good bacteria growing on it. But after several years, exactly how many years depends on each ponds particular circumstances, I think the cons of the accumulated muck will cancel out any beneficial effects the rocks might still have, if any.
Check back with me here in 15 years, let me know if you are still grooving on that rock.

That will give you time to read this blog.
http://www.worldwidekoiclub.org/index.php?option=com_content&task=view&id=101&Itemid=38