Want to reiterate this point. I believe this should be the theme for all machines in Industrialization. Most suggestions are still relying on magic multi-blocks. The reinforced stone block and the filter block are what determine how the work is done not the specific configuration of the overall structure. You've shown us that the reinforced stone/piston configuration is limited only by our imagination (and possibly pointing down). The amount of ore that can be processed is only limited to how large the structure is built but still only based around these two blocks (reinforced stone and piston).
Going off of this suggestion by Kyll.Ing.:
I like this idea but using the theme of having a block that does the work and constrained only by how it does work. For smelting filtered ore you would build a crucible block. You need to heat the crucible. Plop down a log underneath and set it on fire. That's not gonna last very long is it? Ok, netherrack then. But that's just one fire source so that's not going to get very hot, perhaps not even hot enough to smelt the metals. Well, how about lava. Now we're cooking. More lava, more heat. Once you start working with lava you probably want to encase it to make sure it doesn't spill everywhere. Have COFH/TE installed? I bet pyrotheum would really get things cooking. But that's even more dangerous than lava. Hopefully you see where I'm going here...
A couple of issues I just thought of while typing this out:
How do you get items into the crucible without a GUI? That's tough because to stick with the theme I have in mind we don't want magic multi-block structures. Perhaps something similar to the way Thaumcraft uses its crucible. Physically throw items in items get spit back out after work is completed (and my understanding is that this is basically how the Industrialization filter works atm). An Industrialization crucible could work in a similar manner. Throw in ore to be processed and work is completed by time relative to the amount of heat it is receiving from the 5 available sides (as the top is where you toss stuff in). After work is done the processed ore is spit out one side. So you'll want to keep one side exposed so the processed ore doesn't fall into the lava and be destroyed. You can stand on that and collect the items or you can use something to automatically collect them. So many options here.
The majority here seems to wanting BIGGER structures. The above allows you to that while maintaining the same concept of context aware blocks that do work based on how they interact with their environment. Want big? Then build it big. More crucibles, more lava, more hoppers and converyors and bamboozles and whatsits to your heart's content.
Anyway, this kinda went a little longer than I had intended. I think, at least hope, I got across what I'd like to see in this mod