I'm going to detail what I was defending in weardown/breaking machine, when I said it would look like a nuclear reactor guy. But that's surely a huge modification of the current system. Maybe ideas for IC3 ? 
So. Let's begin.
The basic Idea is to create config having different advantages, different cost ... in a GUI. (Because spending time in complicated GUIs is fun ^^)
The GUI would be: 3*3 for a single Machine, 7*7 for a Advanced Machine and 7*(7+n), where n belong to [0;6], depending how many machines are on the sides of the advanced one.
In this GUI would be a few components:
-Engine: This is the base of your config. Each Engine would produce a force that can be used to turn something into something else or to make items (Ores, Coal Dust, etc ...) you want to transform move from a sides to another. This would be used for semi-automation. Each engine produce a basic force of 3N, consuming 3EU/t and heating 1HU/t (to be adjusted for balance reasons with cooling component).
Can Directly Output N for Machine, without Force Transmitter.
-Overclocker Upgrade [Engine]: N produced could be Increased with Overclocker Upgrade (1 per slot in the GUI, so max 3 for one engine, assuming you need to output your Force, if you can cool it), but it would make, as it does currently, increase EU consumption (BUT, 1 Overclocker upgrade = *2 for N produced, *2.5 for EU/t consumed, but *3 for Heat generated by the engine, because of the max 3)
-Transformer Upgrade [Engine]: To keep that system as it is now, each engine could accept max 32 EU/t without any Transformer Upgrade, 128 with one, 512 with 2 won't be considered because of you couldn't use more than 128 with unstackable Module/Upgrade, what I chose to make machine work as a Nuclear Reactor: stackable Items wouldn't change your config for space reasons).
-Cooling component: See Nuclear Reactor.
-Efficienty Module [Engine]: Would decrease the Energy consumption of an engine (Divided by 2 for each Efficienty Module, but at the cost of a newspeed=0*7^numbers of EM*speedwithoutEM (So when using 3 of it, process would be almost 3 times longer, but 4 times less EU-consuming. Note that the speed malus would be translated by a N produced= 3(0.7^number of EM on the sides of your engine). Can be used with Overclocker Upgrade to decrease the cost in EU, but decreasing too (less) the Speed.
Of course, decreasing the N produced would decrease the Heat generated.
(Maybe value have to be reworked)
-Quality Module Upgrade[Furnace/Macerator/Compressor/etc ...]: Increase the chance to get a Second loots. Each process has a second loot (example: 3 iron dusts instead of 2, or one copper dust + 2 iron dust. Depending on wich process, it can be + 1 basic loots or 1 bonus loots. The probability to get an extra loots would also be different in function of the process: getting 2 advanced alloy from 1 mixed alloy ingot would have lower chance than 3 dust to occure)
Of course, this would be something like 2.5/5%* more per Quality Module Upgrade, with a max of 3 Module Upgrade (because one side is taken for Force input).
*Depending on wich process. Without anything, it is 0.
Quality Module Upgrade would decrease the Force by 30% (so, 2 QMU==> -60% speedness, what could be cancelled with OverclockerUpgrade ... if you can cool it and provide more energy), and generate more HU (1/2 of HU generated by simple Engine).
-Steel Gear: Simply, it's something that can take N-Output from Engine and give it to "Machines" [as component, each machine being the thing that can process, if N applied] or to others Steel Gear, if you want to make a chain. Produce 0.1 HU/t per N/t transmitted. Each Steel Gear output the same amount of N per side, and can accept output from different sources (Others FT or Engine).
[Somethings] means that the component affect "Something", and has to be put on a side of this "Something".
-Conveyor Belt: Simply, it can take items from the output of a machine and make it turn to put it as input for another. Items are moved like that: Up, Right, Down, Left.
Using Conveyor Belt + "Relayer" (Name it as you want) (Acting as an input for one Conveyor Belt, as an output for the other, making you able to move Items on more than 3 slots)
Conveyor Belt has a 10 EU/item moved. Can move as much Item as you want per seconds, it would just need more EU. (and Up-->Down is 2 movements so 2*10/items)
Engine and Steel Gear (for macerator + compressor + recycler) have a duration value. To make it unbreakable, just apply continuously Oil cells. The Oil would be consumed faster if Engine are overclocked. Oiling also has the additional effects: speed + 5%, EU consumption -5%.
For Furnace and Extractor (Using sorts of Transformer Module, and cable instead of force transmitter), it's just more coolants items: Heat generated by Transformer Module and Cabke has to be entirely cooled down by near cooling components . (Or find something else)
Notice that the system works in the same way for N produced by engine/ EU output by Transformer Module. That's just Transformer Module turns Alternative Currents into Direct currents, wich is transmitted by normal cable.
Oiling cells: [This paragraph concerns Oiling cells AND Coolant cells, because Coolants cells used with cable/Transformer Module sucks heat from it, and the heat generated by Cable/Transformer Module has to be 0 to make Cable/TM unbreakabke, as I already describe it]
Each Oiling Cells can oil up to 4 components, but it will be damaged faster. Maybe Oiling Cells should give you back empty cells when completly used, maybe not. This is not about what I am argueing. But I guess it shouldn't gve you back anything.
Note that when I say "Coolant Cell", it could be something else with the new reactor components, but I haven't look that much to the new system.
Crafts:
( 
= Nothing)
Engine:
( = Simple machine
and = Steel Gear)
Steel Gear:
This craft give you 8 Force Transmitter.
Transformer Module:
Efficienty Module:
Quality Module Upgrade:
Conveyor Belt:
:Rubber: :Rubber:
:Rubber: :Mining Pipe :Rubber:
:Rubber: :Rubber: :Rubber:
( :Mining Pipe = Steel Gear)
With these crafts, The rest of the machine for Furnace, Exctrator etc ... shouldn't include Circuits/maybe machine block.
I hope I've been clear. Ask me if you don't understand.
PS: Maybe Miner could have a special GUI too, allowing us to custom it how we want ?
This post is probably going to be edited again and again, if I want to correct/add something.