Basically, I think all these methods can be boiled down to a few basic points:
1) Try to figure out the native ecosystem and try to mimic that some way, using similar but useful (edible or useful in some other way) species. Create a working ecosystem!
2) Use resistant (mostly heirloom) varieties and often trees grown from seed (they are cheap, you can plant them dense, the weak ones will die or you can just leave the strongest/tastiest alive). This will make intervention (eg. spraying) less/unnecessary
3) Manage the biomass so that it would speed up the processes of soil regeneration (cutting grass and putting it around trees, or chipping woody biomass down and putting it on the soil, using grazing animals to recycle nutrients, etc). Managing biomass is basically the most important job on these farms. Chainsaw, chipper, scythe, lawnmower, axe, saw, you need all sort of things...
I am also working along those principles and my trees are blooming amazingly this spring: all of them are full of flowers so I now hope for plenty of fruit this summer and autumn ...
And finally, why we ended up with the current setup?
Our current agricultural system is based on grains which are annuals. They can be stored for years (unlike fruits and most nuts), they have a short life cycle, so when you move to a new area (settlers) you can quickly rely on them, and they are a very concentrated store of carbohydrates. So - despite their drawbacks - they are actually great. Unfortunately, they take a lot of work and our current production methods destroy the soil...I am convinced that agroforestry is the future but it might take some time until it becomes widespread...
