I was thinking of a scenario like below. I know Gus's situation is a bit different. In the sketch below, the pond bottom is lower than the discharge area, so by the time you raise the inlet(for flow rates) it would be near the surface. The green line is a capped pipe to force water into the bottom. Do you think this would work in getting the water flow to stay optimal and still pull water from the bottom?
Granted, the inlet of the red pipe line could be just down on the bottom where the blue arrows are and avoid all the fancy pipework upwards. Should still act like a siphon right? But with your comments above about how the drop of water thru the pipe makes the flow rate increase, the lower it is than the outlet it must decrease significantly? Does it drop to where it's like a standard horizontal drain pipe, or does it even get lower than that?
