I'm new to the website too, but we built our first ponds in 1992, and now are up to 18, all with principle spillways being overflow tubes. I agree with some of the prior comments about questioning your contractor. I've had 3 different contractors and they all put in fine tubes. I'd suggest at least a 10 inch tube, to minimize problems with trash plugging it. Every once in a while we have cattails plug even a 12 inch tube in the spring, so maintenance is important. Your secondary spillway is also called an emergency spillway for a reason-- it is only to be used during 25+ year storm events. In addition, this spillway should be vegetated with a sod forming grass that will protect the soil in the event that water does flow though it. Trees on the spillway (and moreso on the dam) are not good, because when the tree eventually dies and the roots rot, they form perfect little channels to breach your dam.

Your contractors idea about building a deep pool at the inlet, then a higher ridge before dropping into the basin near the dam might sound like it will work. However in practicality, if you have sediment enter your pond during a heavy rain it won't settle out in the upper pool. Your best bet is to make sure you have good vegetation cover in the watershed. Otherwise if you finances allow, you might consider a series of ponds in a single watershed, if you have enough water.

Back to tubes, we've used heavy grade sewer pipe for several ponds, covering the outlet and inlet with sections of galvinized corrugated steel to prevent UV damage to the plastic. Rent a tamper and be out there when the pipe is installed. When you fill in the trench, the most critical area is below and to the side of the tube, so fill slowly and pack often. It's easy to get in a hurry and fill too fast, then you could have poor packing below the midline of the pipe. Get good quality antiseep collars and carefully install them. Then we take heavy plastic sheeting and put around the tube on both the inlet and outlet, and cover with field stone.