"I'd like to start working on the intimacy. I think when we're back to where we should be, it'll help her, too, because I'll be more content and more likely to be understanding when she wants to do some of the things she wants to do."
Might be a good thing to say to her (sometime when she's in a receptive frame of mind).
Right now I think she's going through some kind of mid-life crisis; life didn't turn out the way she wanted it to, and/or the things she thought would make her happy did not make her happy. I think she is struggling within herself with respect to how much she wants to rebel.
Meds might be helpful to her, though for that you need a live pdoc who can write up scripts.
I am thinking she is dissatisfied with the compromise you are at, though as you said, that is the nature of compromise: All parties involved give up some of the stuff they want, so that all parties involved can get some of the stuff they want.
She may also be disappointed with her role of motherhood (which then probably stirs up guilt, and puts her on the defensive). It is sad if she can't love her own kids, like she probably wishes she could.
Eventually, she will probably arrive at some kind of acceptance about things. She needs to. This will be a slow process, and you will need the patience of Job. You can look at it and say, "Her anger makes no sense." But emotions don't always conform themselves to reason. Her anger comes from somewhere deep within, buried under its secrets and perhaps bolstered by chemical turmoil.
Life changes; people change. It may be slow change, but tremendous forces may be at work to make the change. Something will calve off that glacier eventually.