There's an interesting BBC documentary series on the planets, called The Planets, that has an episode covering the Voyager probes. They had to do some quick redesigns on them after Pioneer 10 and 11 visited the outer planets and found fun stuff like radiation and unexpected rings. They said that if they hadn't had the earlier probes, Voyager would have been fried when it got to the system.
You might be dead by the time that actually happens, so better to be killed by sorrow of only getting fly-by data than the agony of having only what Hubble and its successors can resolve.
Therefore, the Pu-238 used in RTGs is likely produced through another process, neutron capture in Np-237. Np-237 is produced in very small amounts in a uranium reactor, but as it's the only Neptunium isotope produced in any significant quantity, there's no need to do an isotope separation on it. It can be chemically separated from the other elements in the spent fuel, which is much easier, although certainly still not easy.
In any case, with the end of the Cold War there are indeed fewer facilities willing & able to produce Pu-238 in kilogram quantities. In the US, spent fuel from commercial reactors currently cannot be re-processed at all, due to proliferation concerns.
We just need to start setting up bases!
ALL YOUR PLUTO BELONG TO US!!!