We do married filing separately for almost exactly the reasons you bring up. First big disadvantage is that you cannot write off any student loan interest. Second is that if one of you itemizes, you both must, ditto for if one of you takes the standard deduction. Third disadvantage is a significant limit on IRAs. I don't remember if it's traditional or Roth offhand, but there's one sort that you cannot have of if you're married filing separately.
That said, the 403b gives you a lot of space to put money aside. It's what I'm doing, plus a 457 through my employer, which gives me money that's accessible before traditional retirement age.
So, there are significant downsides to filing separately. There are other things that you lose too, and every now and then I'll stumble across one of them. It's worth looking into pretty thoroughly before you make a decision, but for us, at least, it worked out for the best.