In the first place he is not sad because she did not wait for him, but rather it is his tears of joy proving that he saved her.
Remember that his guy was at his lowest when his mother was killed and he swore to change the future when he recognized he time leaped.
And i love how the main villain of this series showed vulnerability at the end implying that he was never a pure evil type of person.
it just gives depth and perspective on how beautifully written this anime is<3
ps. i heard that in the manga.... the girl really did wait for him but his mother said his life is on 50/50 of chances of waking up..
so she urged the girl to give up on him so yeah that happened xD