I realize that reprocessing is very different and kind of annoying in my mod. Those annoyances reflect the real-life annoyances expressed by my model, but I've sped everything up at least 1000 times compared to any real neutron reactions. Reprocessing MOX does in fact "eliminate" nuclear material as a final stage, by exchanging all of the reactioned material -- about 5% of each spent fuel cell per run through the reactor -- with raffinate, which gets out-processed to plutonium-238 (end product of nuclear production chain) and radioactive glas (also end product of nuclear prodution chain). Processing MOX will require a long and very slow production chain, because a single nuclear fuel unit takes so long to use up, and the REMIX recipe requires a large number of spent units. My mega reactor complex, with 48 reactors, produces enough spent fuel to run reprocessing two to three times per day. I've thought about trying to rebalance this, but the kicker is that as the recipes are now, my model adheres to strong mass and energy conservation principles, hard-coded into my excel spreadsheet, up to 3 significant figures, across every single nuclear object in the game (Except the "chemical" nuclear fuel, which is 1.21GJ as a joke, so I kept that value.). Once I start messing with one of the recipes, everything across the recipe network changes, and this is the best balance I could find. In real life, it takes 9 months to burn down a fuel cell to where it can be reprocessed (More or less: fewer months if you want to make weapons; longer if you want to make reactor-grade plutonium.) You'll need HEU processing/reprocessing, too, so you have material available to "recharge" each MOX cell for repackaging -- that's where the 5% goes in each cell: 5% goes out to raffinate; 5% comes in as new HEU. The plutonium comes from HEU reprocessing. So to even kick start this thing, you're talking about a few days to burn down enough HEU for a reprocess (using PUREX) and then enough MOX for a reprocess (using REMIX).
I've made nuclear fuel about 25 times more energetic compared to vanilla. So I wouldn't worry too much about it (and we don't on our servers). Using LEU in boilers will produce a smaller amount of DU, if you need that for weapons and whatever, and is pretty efficient as it is. HEU is better. MOX is the best, yes, but the reprocess time is just insane. At least I didn't make it 9 months. :) I had to quite literally build a "speed factor" into my model just to make the times reasonable (Under vanilla settings, I think it takes about 1.2 hours to burn down a fuel cell? I use my physics mod, so it's different.) I have plans to make it possible to use natural uranium in a CANDU reactor, which is an option to try to get away from having so much DU. I want to figure out ways to burn down that DU, but, the truth is that DU is not terribly useful beyond as a casing, and it's toxic so I've had reservations about letting people make steel from it, althoug h that may be where I end up.
I think there's a picture on this mod's page that has a full reprocessing chain setup.
