You two would likely pay lower taxes or get a bigger refund if you filed MFJ, the trick is to convince her to do it and to have a foolproof way of splitting the refund. An attorney can certainly help here. (You can't force her to file MFJ but you can try and persuade her based on the larger refund she will get.)
For future years, I actually don't like the idea of splitting the dependents -- alternating years and so on. I've seen too many complaints. The problem is that even if you agree to alternate years, the IRS is not bound by your decision and if she doesn't sign the required form, you have go to family court and ask for an order that she sign the form -- the IRS won't do anything otherwise.
It seems to be smarter to me to simply let her keep the dependents in every year she qualifies (assuming she gets majority custody) and instead, negotiate for a lower child support rate. Every other year when you could have claimed the children, instead your child support is reduced by $2000 per child.
That way you aren't dependent on her to sign a form for you every other year for the next 21 years.
(Just my opinion, I'm not a lawyer.)
