Pipe should be strait and the more sloped it is (greater the drop), the more water it will carry when full of water. The amount of freeboard that is needed depends on the watershed, rainfall amounts, pond size, pipe size, drop on pipe, pipe material, and length. There are formulas to size and design pond drains, dam height, and emergency spillways. I just over-engineer mine.
High spots in a drain pipe can cause an air lock. A 3" pipe is very small for most ponds. I have 4" drains on a few of my wetlands but will never go less than 6" on any new ones after having turtles plug the 4" ones several times. Even had a turtle plug a 6" drain. I now have guards on them all.
