I play on a Monster Multi-Player server and have just put the final pieces on what I would consider my completed Applied Energistics storage system. If I had to rate the mod, I would give it a 9/10.
Applied Energistics, to me, is a must have for late game FTB. Why? Simply because it is one of the most important steps to optimizing your time in late game FTB.
Lets start with the crafting. Applied Energistics offers two important machines that speed up crafting. The first is one of the most basic machines, the ME crafting terminal. The terminal itself is your basic 3x3 crafting grid with a twist. While crafting, you can have access to all the items in the AE system. You don't need to find out how many items you need for a recipe or run back and forth between chests to get what you need, if it's in the system you can use it. The ME Crafting Terminal ISN'T a late game item. In fact, I would consider it part of the mid-game. It is cheap and can save you hours of time you would have normally spent crafting. The next important addition AE adds to speed up the time it takes to craft items is the Molecular Assembly Chamber. Let me just take a moment and catch my breath, because this is going to be important.
The Molecular Assembly Chamber is, to me at least, the single most important item in keeping up with crafting, item supply and item management in late-game FTB. The Molecular Assembly Chamber is a multi-block structure capable of making practically every recipe in any FTB pack. To add an auto-crafting recipe all you have to do is teach it how to make your item through a blank pattern and place it in the assembler. If you have to cook something for the recipe, you can teach it to do that by placing an ME interface on any furnace you can insert items into via pipes/item ducts/etc. Do you need to compress something? Put an ME interface on a compressor. Need to fill redstone conduits with molten redstone? Set up your ME interface to melt down the redstone for you and put it in the conduits with te3. The auto-crafting possibilities with AE are endless. There is a way to automatically craft just about every single item. And when you want that item crafted, it's as simple as as telling your assembler to make the item through any terminal or wireless terminal, putting in a number for how many you need made and waiting for it to make them. The Molecular Assembly chamber has saved my friends and I hundreds of man-hours of work in crafting large amounts of items we need to continue advancing our technology and staying on top of things.
The molecular assembler is also responsible for keeping the base running with minimum human intervention. The assembler makes fertilizer for auto-farms and automatically restocks them. It makes bog-earth for peat farms and makes sure that the farm never runs dry. The system stores, organizes and is configured to automatically refine all the ores we mine. We don't even need to be at the base to refine and store our ores, we just hook the AE system up with an Import bus to an ender chest, put down a chunk loader and let the AE system do the dirty work while we stay out mining. At the same time the system is also keeping the quarry in check, efficiently and effectively making sure items go where they need to when we want them to.
The only downside to AE that keeps me from giving it a solid 10/10 is that any items with damage values tend to clog up the system, so it becomes a pain to store damaged tools into the system without clogging it up and taking up an entire type slot on a storage disc.
TL;DR: Very good, 9/10. AE is the superior late-game storage and sorting option and is a must have for time-efficient bases.