Could you add a "Processing Controller" which would work like the Cobblestone Controller, but instead of the cobble-gen it would have some input slots, 4-5 upgrade slots and a circuit slot (like the conduits have)? With something like this we could make a Octuple Compressed Cobblestone much smaller or make a ore processor (grinding and smelting).

As a circuit would suggest all the enderio upgrades (like speed and item-filter, ...) and a parallel upgrade, which would allow the user to select multiple machines that can receive items from the input slots.