I hear you on all of this -- it's beyond me how Turbotax can literally ask who is associated with what income and then get it wrong on its very own what-if form. One thing you can do, though, is modify the what-if form. If TT puts all of an amount in the taxpayer's column but it's actually split between you two, you can change the amount in the taxpayer column and it will put the rest in the spouse's column. (Or something similar -- I haven't worked with that form in a few months.) And you can add and change and delete amounts wherever -- doing that gets me close enough, so it may get you close enough and then you don't have to do two whole sets of tax returns and compare them.
Though I'm thinking that you could actually create the two returns in TT without too much trouble. If you first enter all your info and tell TT you're filing jointly, print out the final returns as PDFs but don't file them, and then go back and tell TT you want to file separately (just switch that option but have TT use all of the same data), and print out THOSE returns. Compare them, and then tell TT the way you have concluded is best and go ahead and file. Nice thing about robots is they don't get mad at you for being wishy-washy.
