A feature that's been in Mekanism since before I was involved, but that everyone seems to forget about (including me, often) is ComputerCraft support. A LOT of our machines work as peripherals, including Energy Cubes, so you can just stick a modem on there and program away, use redstone signalling, whatever you want.
Would be nice to have some kind of Mekanism-native block-based monitor for things, though, for the less programmatically inclined. Maybe something that could be stuck onto transmitters as well, work similarly to the item-form network monitor and be able to emit redstone signals based on transfer rates or something. On which note, some kind of "information transmitter" could be cool. Something like MFR's rednet, maybe?