I too have tons of leaves falling in the pond in the fall and the oak leaves all winter and then the oak leaves melt through the ice at ice out too. Your pond and my pond are not too large that we can't rake the edges and get a fair number of leaves.
In the spring at low 'tide' I used to rake by throwing a landscaper's rake with a rope out 6-8', with the rake weighted down with weights. I would drag it back and and can clear out hundreds of pounds (wagon loads!) of nutrients, decomposing leaves, last years FA, etc. I can't do much about the deep layers and yes the leaves tend to build up there and go stagnant, turn black, smell!
I run aeration in summer only. I'm toying with ideas to stir up the bottom in the deep (trash pump, mechanical agitator, towing a box spring through the deep once in a while etc) and continue to aerate.
There are threads here about setting up some snow fencing in the fall to prevent leaves from blowing in but most of mine fall from above.
I think in the deep without mechanical agitation and aeration the leaves will not break down much, they seem to be preserved in the cold anoxic water. Although my aeration is in the deepest point, the bubbles go up and I'm not sure how much the water is stirred right at the bottom at the leaf surface. Certainly when the leaves are 18" thick you need mechanical agitation.
Bird poop and phosphorous in fertilizers is a tough thing to combat. I believe our region, or maybe State has a law on the books that only phosphorous free fertilizers are allowed.
However, this year no matter how tempting it is to rake the edges, I'm waiting. The FA that is there and the sticks and leaves are the only cover my micro-organisms have. The perch fry, the tadpoles, the toad-poles, the minnow schools, they all are in the shallows and I don't want to rake them out. I love the sandy bottom, clean swept look all around the edge but maybe I'll go for that look later in summer when everything got a good headstart on growth.
