Mean that you have an upper limit on what you can store. For example, I'd like to have a DSU full of wood, feed a solid fuel boiler, and never overflow into the world. Doing this with AE intelligently is hard.
Even worse, level emitters are binary; on or off. This means that if you DO want to say, limit the amount of MFR rubber you have in your system AND the amount of rubberwood? You need 2 export busses and 2 level emitters. Look at Dire's current build on his SMP server and note that not only is it going to totally destroy his flagging power reserves, it's going to be a pain to extend if he ever wants to use apples or saplings in another way.
Applied Energistics is terrible for input processing. It's great at storage and auto crafting, though. But if I am wrong, Hydra, please tell me. I'd love to know how to do this stuff with just AE. It's way more convenient to use unified piping. It's one of the reasons I love Infinitubes.
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The big problem with RP2 was that it would only do even splits. You couldn't send 3/4 of your wood one direction and 1/4 another way unless you made unnecessarily verbose builds.
Kirin you can use a fuzzy storage buss against a deep storage unit and it acts in the access terminal like its in the AE network. Shows the amount is super fast to access etc... I am now using a hybrid system of AE and deep storage units. Its allowing me to spend more resources on automation and cables then on storage cells. Anyways just a heads up..