I just went through some of your old posts. I could be completely wrong, but I'm going to share my take...
One thing you have to keep in mind is MLC is a like a wave you just have to try and ride out. It's not anything you can hurry through. And, from what you've described, I think your wife is probably still in the midst of it, and I think you have been holding onto some unrealistic expectations.
In fact you both seem to have high expectations of each other. My guess is you're expecting a realtionship closer to what your parents had and since you haven't been seeing that you've been holding onto some disappointment and resentment. And I imagine your wife senses this. I'm going to guess she also feels disapproval and a lack of support from you for her lifestyle choices (i.e. career over family, religious non-conformity or questioning, etc....). Even though I can understand your disappoval about these things (they wouldn't be my choises), sometimes our spouses do make choises and go in directions we don't particularly like or agree with, but to be content in marriage we need to let go of our own personal expectations and accept our spouses for these ideosyncracies or life choises. In fact, I think we sometimes need to stop for a moment, look at our own personal prejudices and do a little mental 180 and begin trying to appreciate their differences or adventurous spirit.
Have you been interested in the things she's doing? Have you been supportive of her decicions? (I'm not blaming you here! Just trying to get you to look at this from another perspective). I know she's done some nutty things, like get you into this whole parenting thing and now has kind of jumped back towards wanting career fufilment, but quite honestly it sounds like you had the more loving family background, maybe you are meant to be the more involved parent with your boys? At least for now. It sounds to me like she didn't have great parental role modeling, she may be feeling like a bit of a failure in the whole mothering thing and that might be why she's pulling away from it. Do you think she might have been needing more support and encouragement from you? That's not an easy thing for most men, but you do seem relatively in tune with things.
Anyhow, I hope you are not offended by this post, I'm just trying to offer another perspective that may help give you some insight... or I may be completely in left field!
There is no arriving, ever. It is all a continual becoming.