This idea was prompted by a discussion going on elsewhere in the forum, so credit to Bluehorazon for sparking the idea and getting me thinking about the specifics of it.
As of right now, once a player has enough of an energy surplus and scrap surplus to produce a mass fabricator and keep it running and supplied with scrap full time, they've pretty much got it made. A couple hundred solar panels, a wind farm, a reactor, and a cobblestone generator, and you can just sit back and watch the UU matter roll in, then produce as many diamonds as you want from that! Or you can craft the whole quantum suit! Or...well, then what?
Now, bear in mind that the mass fabricator is essentially creating matter from energy. This takes it out of the realm of science and quite healthily into the realm of SCIENCE! And when you're playing around with the laws of physics...things should not always be cut and dry.
I propose that we add a bit of a "mad scientist" feel to mass fabrication. For example, you let the mass fabricator run, and instead of producing UU matter, which can then be used with a reliable recipe to create whatever you want, after a certain amount of time it produces something random. The amount of energy consumed should be proportional to the item created, so if it creates a block of wood it should do so after only eating maybe a thousand EU, but if it creates an iridium ore, it should consume millions. If left to it's own devices, this continues, for as long as the thing is powered...every once in a while, it spits out something random. Or, some random event occurs...like, for example, one of the ideas that Bluehorazon had given would be for a dozen chickens randomly appear out of nowhere, because the mass fabricator randomly created them. Or a freak snowstorm in an otherwise temperate biome. Or, in a rare event, a nether portal is opened nearby, or perhaps just a rift big enough to let a single ghast loose to wreak havoc in your factory. Who said SCIENCE was totally safe?
Now, the mass fabricator's UI could also have an input slot. This input slot could be filled by an item that you've previously acquired before, making it sort of a "target" item. Putting something in the target slot would greatly increase the chances of the mass fabricator replicating that item for you, at the standard energy cost of the item. However, it could still potentially freak out and give you a random item, or a random event, because when dealing with weird science, nothing should ever be certain.
Now, the kicker. This would allow for truly "secret" recipes, something that a crafting guide plugin could not teach you how to make. You could potentially add new and interesting things to the game, and the only means of acquiring these things are to play around with your mad scientist's toy and see what happens!
This would give players a reason to build mass fabricators, a reason to keep them running, a reason to make sure they're well enclosed and defended, remove the tedium that starts to set in once you have a few stacks of UU matter crafted, make quantum equipment harder to get and therefore a more attractive (and well-deserved) goal, and give a way to add truly secret stuff into IC2 that can't just be plugged into a workbench in a certain recipe and give the same results every time. In short, it would make the endgame of IC2 a lot more entertaining, because even with a full workshop of advanced machines and several nuclear plants operating, you'd still have something to do, because who knows when you might discover something you've never seen before that's been hidden in the depths of IC2's bag of tricks?