To be fair, Throne of Bayonets did have a pretty BLEAK premise that pretty much permeated throughout the fic, and it's hard to say if Asuka and Shinji were in a better position at the end then when they started. Even Shinji pretty much asked himself "How long can this "relationship" last?" at the end. So, it makes sense for Crown of Stars to go in the opposite direction, though I can't be a critic of it yet as I haven't read it all the way through, but it IS on my "To-Do" list.
Genocide however, is a good balance between Bleak and hopeful, as both Asuka, Rei, and Shinji are in a much better place they were at the beginning, but it wasn't without some pain and sacrifice. It was a healthy balance of struggle and hope.