I think that's a fair suggestion. I see that Pahimar is going with the old tried-and-true method of crafting recipes for EE3, kind of like what the old EE had before the transmutation table was created. While I agree that EE2 did make almost all projects obsolete, simply making things more expensive and then offering a chance at a discount may not be the solution.
If for example, I wanted ender pearls to research in Thaumcraft, (or use for some other purpose) I would need quite a few of them. I most likely have not been to the End in order to obtain end stone. Therefore I would have to get 21,024 EMC worth of some item that is easier to find, but still costs enough to reach that goal quickly. I'm certainly not digging up 21,024 cobblestone, and to make one from iron would cost about 82 iron. That's about a stack and a half of iron for a single end pearl. And to produce them in moderate amounts would be ridiculously tedious and time consuming. I may as well go out and kill some Endermen.
Overall, having a bottlenecked discount to a ridiculously expensive item is probably going to be annoying if you don't want to track down a stronghold (which I haven't accomplished yet). Instead, crafting recipes should be used to only allow a few items to be used to create rare items instead, so finding exploits would be much tougher, but at least it wouldn't be so expensive to produce, and isn't cheap enough to mass produce in a magical box that creates matter out of energy.