This is an issue that DDOT has been looking at for a while. I believe they've changed the timing of the lights during the weekday so that traffic has more time to get through, but you're right, on weekends it still backs up very badly (especially on Sunday when the right lane is filled with cars parked for the church there). Longer term, DDOT is looking to totally redo this whole intersection and allow southbound traffic on New Jersey Ave to continue through NY Ave, making NJ a two-way street on that side. That'll ease up a lot of the congestion on 3rd, and should also help adjust the timing of the lights.