Nuclear waste disposal
Let's admit it, uranium endlessly disappearing into reactors is unrealistic. What I'd like to propose is introducing a risk & reward system to nuclear reactors in the form of nuclear waste disposal.
This system would introduce a new block, the nuclear waste container. This block would need to be connected by conveyors to the reactor in order for the reactor to work.
The waste container would very very slowly fill up, the waste being an intangible resource similar to oxygen and hydrogen.
When full, the container would need to be switched to keep the reactor running.
Unlike regular blocks, the waste container would not break completely when damaged, but would instead become a leaking container, creating a spherical radiation gradient hazard proportional to the amount of waste inside and the damage to the container. If inside a sealed airtight area, the whole area would become flooded with low levels or radiation. Intense radiation near the broken waste container would also cause blocks with computers to stop working, creating an interesting engineering challenge for cleanup. Players would of course be damaged by radiation, with the damage slowly tapering off a while after leaving the radioactive area.
The containers could of course be used as nasty radiological weapons, as dropping them on your enemy's base is always more fun than being responsible and burying them somewhere.