This is tough – please anyone feel free to offer a different suggestion than mine, as I could see arguments for any of them.
That said, I think Permission fits really well as the Overall Story Issue. All the characters are conflicted because of limits they impose on themselves, or limitations imposed on them by others. Think of how Rich really struggles with the limits others place on the job he can get, and then overcomes those limits by giving up his own self-imposed limits, giving up his conscience & following Cromwell.
Then you have More, unable take the oath because of the limits of his conscience.
And at the highest level of what’s driving the Overall Story, King Henry has limits both within and without. He wants to legitimize his new marriage; in that sense the “Bending to the marriage” is actually a type of permission he requires. And Henry would illustrate the counterpoint of Deficiency very nicely, being motivated by what he feels he lacks – a male heir, a happy marriage. (note: if Permission is the OS Issue, Deficiency is the counterpoint)
EDIT: King Henry has self-imposed conscience-based limits as well; at one point More mentions that the King would never perjure himself.
Here is a nice quote summarizing an OS Issue of Permission:
CROMWELL: Unhappily [More’s] innocence is tangled up in this problem
that you can’t change your woman without a divorce
and you can’t get a divorce unless the Pope says so.