Actually I see a lot of things I would change on both of your lists but, like all such comparisons, it is very subjective. And while I applaud your effort and ingenuity in creating these, I don't think the scores (as you've obtained them) are meaningful. There are too many "apples and oranges" comparisons in terms of where you obtained the scores and the arbitrary choices you were forced to make.
For example, I don't understand the reasoning behind dropping Rust Belt prison out of the top 15 just to keep Five Tigers together. Only one of those missions scored higher than RBP so why are the other two included in the top 15?
I realize that these kinds of arbitrary decisions must be made sometimes and I'm not faulting you for it. I just don't think that they lead to reliable scoring. For instance, I can't imagine any reasonably accurate scoring system leaving "When Still" out of the top 10, let alone as far down the list as it is.
That said, thanks for doing this. I really appreciate the effort and it is helpful, at least for getting a general look at how FMs fared.