I am a huge proponent of gravel bottom ponds. The mini pond has a fully graveled bottom. and my large pond has all of its shelves with gravel and the deeper 3 foot area is bear liner. However, after seeing how well the shelves have done with gravel the past 3 years I am planning on getting in and placing gravel on deep area of my pond as well. that way plants can be better established at the deeper levels and have rocks to root into.
From what I have seen gravel does great in that it gives additional surface for algae and beneficial bacteria growth. It gives hiding places for small organisms that the fish in turn enjoy hunting and searching for. And most importantly it gives a good substrate for plant roots. I have my pond just about fully planted. I love the natural look of the plants rather than rocks everywhere. On 2 of my 3 shelves you cannot even see the gravel bottom as it is completely grown in by versalles grass which the fish hunt in constantly for bugs and tadpoles. They also much on the grass in the afternoon.
However, please keep in mind that I do not over feed my fish, i don't have 2-3 foot long koi and my pond is a sustainable ecosystem pond with no chemicals and no mechanical filtration. This is how I wanted it and was my choice. If you are wanting a pond to house large koi that you wish to see at all hours of the day and keep nice clean rock ledges and sides and maintain water quality with a UV light or chemicals that will result in large wastes from algae kill offs than it may not be the right choice for you.
I love it and would whole heartily suggest it for anyone with an ecosystem pond.
Hope this helps....