Ayu would be my choice if I had a gun pointed at me.
It is true that Nayuki may have been a reasonable choice as well - she is his childhood friend, a great person, was there for him in the end when he needed her - but even if the anime had been slightly tilted in Nayuki's favor I still would have chosen Ayu.
She brought me joy in every single scene, I was broken when she left Yuuichi (both times) and I truly, truly
love her character too much to give a damn about the fact that the way everything worked out in the end is a bit of a stretch or perhaps even cheesy. That was the end I was hoping for and it made me very happy.