On a pond, it is a matter of maintenance. Leave enough room to mow and access the pond edge. On a stream, pick the inside of a curve and know that it can still erode over time so you move back farther.
We just used what is called surge stone in SC. About 4" stone. I would cover the end of the 4" stone in the pond with some larger stone just to keep it stable. The rocks that open to the pond should not be covered in geotextile to avoid the clogging of it by iron bacteria over time if that is a problem in your water and soils. The problem with a pipe to the pond is that it can bring in sediments, algae... If you want to use a pipe, be in the 2nd thermocline of the pond which is roughly from 5' to 10' below the surface. That is the better quality water without the floating trash. Below 10' you will get more odor and off taste. Use some filter, an elbow or something to try to keep it from being a trash problem at the pipe intake over time. At a fish hatchery, a solid pipe went into the pond, a flexible hose was added and a filter was on the end. They could lift the filter and clean it as needed. That is an additional cost deal.
Using a trackhoe, the trench was generally 3" wide. You can let the grade fall towards the well to enhance flow. Using stone, as described, allows about 33% pore space at most. So it might look big but it is not as much flow as you might think.
We don't have frost level here except for a few inches. But you do need the water where you pump to stay fluid.
Water flow through the rock versus pumping rate. This also ties to access. Use as big of a diameter pipe for the well as you can. It stores water like a reservoir in that bigger area. And if you go big enough and you ever need to get to the bottom and service the system - you can.
