I don't like the floor in the mainstage area, for one thing. It's not hard wood and if I'm standing on it for more than two hours it starts to bother my shins/arches. Sound Quality is another. At the 9:30 (probably the best venue in D.C. in my opinion) I could be standing almost anywhere in the club and still get practically the same level of music, with limited background conversation filtering in. At the Black Cat, not so much. During the mum show, because of how quiet some of the instrumentation is there were a number of points during the show where I was hearing more people talking than I should have. And during a recent Ambulance show I kept getting bits of sorority girl giddiness from across the room, particularly during "Michigan" and "The Ocean."
If the choice came down to it, since their schedules are almost identical, I'd probably just trek the 30 miles to Baltimore to catch someone who's playing the Black Cat at their show at The Ottobar.