The ending was shit. Sorry, they BOTH should have dissapeared.
Anyway yuki found out that kyon had given her his heart in order to stay alive. Didn't work out, but then when she says "i love you" thats what it took for her to go.
But in retrospect that was pretty lame considering kyon had to stay there and what the fuck is this "rebirth" shit. Its so lame.
I personally think halfway through they were like "SHIT WE GOTTA END THIS" and they tried to end it quickly spending the least they could.