Been using this for a long while. While applied energistics is king, it's bloated and takes far too much time and CPU/RAM I'd rather spend on more enjoyable mods. Posting because although you have said this mod is feature complete(heresy! :P) I do have one suggestion that might or might not be fun to code in.
Linking to containers. Right now you can pull from one inventory, but that means always keeping it stocked with multiple items that are rarely related storage wise, and it has to be placed on that container. So my suggestion is to make a Super Linker, or whatever lol, sneak-right-click a crafting frame, then sneak-right-click a container/barrel and it links the two. Allow multiple links so a frame can pull all materials needed from a players storage area and the time spent in the crafting room is squashed ten fold. Thinking on drawbacks to this would be managing those links. To keep it simple and uncluttered, maybe a second button below the "pull from player/inventory" button could be a "clear links" button. I can't imagine needing much more than that. Shouldn't be any laggy ticks, just a quick for loop going over the linked containers until it finds all the materials needed if their not in the players inventory.