I have made four trips to DC over the last month and flying into and out of National has been a breeze!
I never had to deal with parking at National as I used hotel shuttle or Metro to leave and arrive, so I don't know anything about that.
As far as the bathroom thing, unless you are the very last one on the plane before they close the doors, you should have time to use the restrooms on the plane before you leave.
I don't know when your flight is, but here is one thing I discovered my last trip home this past Sunday.
I finished work early in the day and headed to the airport early to try for an earlier flight or standby. They weren't able to offer that, but they did let me check my luggage in at 12:30 noon for a 6:05 pm flight. I then hopped back on the Metro and went to Pentagon City mall and wandered around there for a few hours and had a nice lunch.
I arrived back at Reagan with about 45 minutes before my flight and was able to get through check-in and leisurely walked to my plane. No rushing, no sitting around the stupid airport. It was really a pleasant experience. The only thing that would have been easier would be if lockers were still operational, then I wouldn't have had to worry about my laptop.
Another thing I would highly recommend is that "all" of your luggage have wheels, even bookbags and diaper bags. Lugging something on your shoulder, even for a short time is awful in my opinion!
Hope this helps!