It's an evolved variant of the concept expressed by Logistics Pipes. This seems very desirable to me. Probably what people are stressing about is that a unified version of logistics pipes without the limiter of chest storage shoots a metaphorical broadside into every other item transport method. Imagine an ore processing and sorting system based off this mod. While expensive, it would essentially be homogenous; an input ender chest and a few paddles attached to machines. Boom. Obama does the exploding fistbump to you as you solve the nation's logistics problems and finally fix those bridges.
That said, I'm really confused by some of the features in the mod. For example: why would you ever want multiple networks? Seems like the disk formatting would let you deal with potential issues there far more eloquently. The only thing I can think of is that huge inputs like multi-quarries might be segregated from the main network so as to prevent them from filling up your storage disks with garbage.
In a game I recently scrapped, I actually did have quarry input be completely handled by AE, from ore to ingot. You described its superiority over other mods quite well.
As for the multiple networks, I've found that you can sometimes run into problems with certain things with competing usage in the same network. For example, getting lead dust for batteries out of a quarry processing network that automatically smelts dusts into ingots is impossible, and I can only imagine what could happen if you automatically compressed ingots into blocks...
However, honestly, those can be relatively easily mitigated by simply doing certain things manually.
Additionally, I suppose if you need an extension of your current network far away, it may be better to make a new network with enderchest linking the two or something, rather then potentially spending a large amount of extra energy per tick with a long cable.
