I was a massive fan of Babylon 5 which had some fantastically conceived plot arcs, but I don't remember finding them as frustrating as this!

Same here. I also thought about the comparison to B5 yesterday (especially with the Doctor/River first kiss and the mysterious person in a spacesuit thing), and while my memories of actually watching the show on TV rather than on DVD are a bit fuzzy except for the Z'ha'dum cliffhanger ending, I agree that the balance between the overreaching arcs and the pay off of the episodes themselves was much better there.