After reading your remarks, I went back and looked more carefully at the EPA proposal. It is a long repetitive, somewhat confusing document, but I believe it boils down to the following.
First, it's important to distinguish two things: how the EPA comes up with their goal for each state, and how each state can achieve their goal.
1. How the EPA comes up with the goal.
In a nutshell, I think they do this:
a) add up all the CO2 emissions in pounds from the electrical sector in each state
b) add up all fossil fuel generated electrical energy from the state
c) take the ratio of a) to b)
That's the starting point.
They then do the following calculation to determine what each state's goal should be.
a) assume that the existing coal plants in the state are made ~5% more efficient (reduces the numerator)
b) assume that existing natural gas combined cycle plants are used at a much higher rate (~70%) than they are now in lieu of coal (reduces the numerator)
c) assume that the 6% of nukes that the EPA figures are due to be retired are not retired. Assume the 5 new nukes that are being built now are finished. Both these energy generation terms are added to the denominator. Assume that new renewables - wind and solar - are built each each from 2020 to 2030 at a rate which the EPA thinks is feasible and add the energy generated from these to the denominator.
d) assume the state implements an energy efficiency program and add the cumulative energy savings (1.5% per year) to the denominator.
The ratio calculated in this way is the goal expressed in terms of CO2 intensity - lbs/MWH.
The state then has a choice of trying to meet the intensity (lbs/MWH) goal, or the equivalent goal of a fixed emission in pounds.
2. How the state achieves its goal. The document repeatedly emphasizes that the EPA is not dictating to the states how they should meet the goal. All they care about is that the state has a credible, enforceable plan which meets the goal. So if a state comes back and says they are going to meet their goal by in part building new nukes, the EPA would be fine with that. They say this very explicitly on page 39:
"States may also identify technologies or strategies that are not explicitly mentioned in any of the four building blocks [basically points a,b,c,d above] and may use those technologies or strategies as part of their overall plans (e.g., market based trading programs or construction of new natural [gas] combined cycle units or nuclear plants).