Here is an old thread about rock lining a pond. It might have some ideas and has some links to other threads.
Rock lining a pondIn our area with naturally acidic soils, using crushed limestone mostly tends to be helpful because our ponds need limestone for Ph neutralization anyway. I used various sizes of crushed limestone rock in all my ponds to varying degrees for various purposes.
Personally I would not worry about filling gaps of current larger rocks. Like Snipe said, good habitat for various critters and fish. I would just add any additional adjacent to or in different areas as an addition rather than a topdress of current rocks. As far as weeds, any short term benefit will be short lived. Eventually silt covers up everything and weeds will grow anyway. It might help a year or two, if any.
