Interesting points, Sean. The principle, to me, is that it is up to the dojo Sensei. It's his dojo so he gets to choose. If that means t-shirt, hakama or running shorts so be it.
As an aside, in Yoshinkan aikido, hakama are rarely worn and I have often trained under a 6th dan who did not wear one. Although we are a yoshinkan club and wear hakama at shodan, and sometimes at kyu grades.