To elaborate a bit:
1. Getting plutonium with Cerys is its own mechanic (that I am yet to discover, haven't played the mod myself, just a little sandbox looking), in PE it's collected from depleted nuclear fuel.
2. Nuclear breeding is an emergent mechanic in Cerys, as opposed to being a separate nuclear 'branch" in Plutonium Energy
3. Nuclear weapons are slightly different, Cerys has both an atomic rocket (hydrogen bomb) and an artillery (neutron bomb).
4. Nuclear waste reprocessing in Cerys is done without the weird barrel carousel, as they did actually make centrifuge have fluid I/O and it looks good
So other than 1 are just more elegant and simple executions of the same ideas. I might be harsh on myself and my work, but I don't understand what people want from PE+Cerys.