I saw the first performance of the tour, in Schenectady, and while I want to make allowances for it being the first time in front of an audience, I generally agree with your assessment.
I thought some of Elliott's choices were brilliant, like the way she used the boxes. The first act worked better for me than the second. I thought "Getting Married Today" was perfect and made lots of sense for a gay couple - maybe even more than it did originally, since for so long same sex marriages weren't allowed.
The second act, though...I don't think the men would have been the ones to sing "Poor Baby," I don't think Andy needed to be quite so dumb, and Joanne proposing Bobbie sleep with Larry felt just weird to me.
I have a woman friend, though, who saw the tour and found that the gender swap really resonated for her, though. It may just be a matter of what we bring to it based on our own experiences.