I am exploring the use of Bluetonium. I have used other nuclear mods and based on that experience, I have a couple of questions.
MOX and Plutonium fuel cells have the same recipe but the MOX fuel cell is 8GJ and the plutonium fuel cell is 4GJ.
Why is the plutonium fuel cell half the energy of a Uranium fuel cell?
And then why does the nuclear and plutonium fuel the same energy?

Why is the plutonium fuel cell half the energy of a Uranium fuel cell?

It's a game balance thing. The plutonium fuel cell is primarily used for plutonium breeding. When you reprocess a depleted plutonium fuel cell, you get back more plutonium. On the other hand, the MOX fuel cell doesn't give back much of anything, so it has to be more useful somehow too.

And then why does the nuclear and plutonium fuel the same energy?

Sorry, I don't understand this question.

My expectation was that plutonium things would be upgrades to uranium things, so I was expecting the plutonium fuel to have more energy than the uranium fuel.

No, the big advantage to plutonium in this mod is that it's easier to get as a result of nuclear reprocessing, which you can then use to get more plutonium. It also makes much cheaper atomic bombs. For the sake of compatibility I didn't get rid of Kovarex but you can disable it with a setting, and maybe even when it is on I should nerf it.