At first I thought that this was an annoying limitation of Applied Energistics but since then I have thought more about it. Instead of putting the ME into a machine, you could put it into a chest and then have a third system take from the chest and do stuff that is way more complicated that can be done with just one machine. You can also exploit this to do efficient parallel processing for slow things like compressing, or getting coal coke. Another useful consequence of this is that you can have a pattern for cobble into glass that inputs with an ME interface into a pulveriser which itself outputs to a furnace. This can output into an import bus although it would probably be more material efficient to have the furnace dump into a buildcraft pipe which pumps into the original ME interface. Alternatively, you could output into an enderchest that is connected to your AE network.
For your IC2 machine there are three good options.
1. Attach an import bus onto the side of the machine. This has the advantage of being simple and contained within one mod, but even basic import buses are expensive.
2. Use a wooden pipe to extract from the machine with either a redstone engine or even better, an autarchic gate. If you use an ender chest to import items into your AE network then you can just pump from that wooden pipe into an ender chest on the same colour frequency, or you could loop the pipe up into the ME interface. Unless an ME interface is configured to have stuff in its inventory anything you put into it will be sucked back into the system.
3. If you have gregtech installed there is an upgrade for the IC2 machines that autoejects about once a minute (I think that is the correct timing). Using that will allow you to autoeject into that ender chest, or possibly even right back into the ME interface.
Hope that helps
