I see leaves on the ground now, and the trees are almost bare. If you have a magical way to keep them out of your pond you should tell everyone here how you do it... A skimmer is something you will want to have. With all the leaves that will not be caught up by your large volume skimmer, they will settle to the bottom of your pond. How are you going to get those out? You mentioned low maintenance. A rock bottom pond is not low maintenance, no mater what the Aquascapes people say they can sell you. Chemicals are their solution and a yearly drain and power wash. If that's low maintenance I'd hate to have a high maintenance pond—whatever that might be. So forgo the rocks, and give it a chance without them. After a year if you really think you want them then you can drain the pond and put them in—as if it was a yearly clean out, so you can get a taste of what that is like.
Oh and the two feet deep, yes Aquascapes insist ponds don't need to be deeper, but that's because they are heavily influenced by the raccoon lobby—they dump tons of money on pond legislators to keep pond depths at a minimum—so raccoons and other critters can feast upon the pond inhabitants... It's up to you, if you want ALL your fish to be feeder fish go for it.
A bottom drain w/4" drain line to a settlement or vortex filter is going to be a must have, and rocks will impede the drain working well—I know cause I had rocks. If you want the pond to be cheap then think about an external pump. They will last longer and cost a whole lot less money to run. But yes, they will cost more to buy in the first place. It's the heart of your system and money spent here is well worth it. I should know I bought a cheap pump, then replaced it in five months, and eight months and...
As for your stream when shut down. You need to calculate the total volume of your stream then provide an empty container or (pond) at the bottom to take up that flow when it shuts down. Run an overflow pipe capable of flowing at the rate of your stream from the pump container at the bottom to the storage container. That would require a sump pump or a separate piping system driven by your pump to retrieve the water.
It might involve a little more set-up money (two pumps) but you might want to consider two separate systems. One being your pond, falls, and filtration, and one being the stream and pump chamber.
I don't claim to have the answers, just throwing ideas out there...