Should I stay or should I go?

So here's the deal, my wife is 8 months pregnant but I'm incredibly unhappy in our relationship. This is not a sudden thing neither.
I'm not going to publicly degrade her by bringing up her faults, but lets just say that the compatability just is no longer there.
We dated, got engaged and married after a whirlwind courtship of roughly 5 months (3 of which I was overseas for work). At the time I had just come out of a fairly long term relationship and I guess it was a combination of not wanting to be alone, having a rebound and lust that guided my decision to propose and for us to get hitched.
She had two kids already and I have taken them on as my own (which makes this harder cause I love the little buggers), but coming from a broken home myself I know that having two happy homes is better than one that suffers.
I've tried making it work between us. Counseling, mediation, spoken with my chaplain, you name it. But she still doesn't get it. I need a partner, an equal, a yin to my yang... what I don't need is a subordinate, someone who just doesn't seem to get it... if that makes sense.
The communication is gone between us and it's just arguments now that fill the voids between the bitter silence.
I need to know if this is the right time to leave, or do I stick it out and hope for the best? and, how do I go about it if I should go? Me being in the military means that she'll lose the house, me, I'll be fine, but soon I'll have a baby of my own to worry about and being a bloke with depression and PTSD, well this puts me in an awkward position.
Has anyone been through a similar situation?
Any guidance would be really helpful.
Thanks GaG community for your help.
Should I stay or should I go?
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