After watching the series and researching it on the internet, I have found these pieces of evidence that show that Heero and Relena are destined to be together.

1. The fact that throughout the entire series, Heero and Relena kept saying each others names.

2. The last scene in Endless Waltz, where Relena is holding Heero's head against her chest.

3. The fact that although Heero is the perfect soldier, he never was able to kill Relena, something that should have been really simple for him to do.

4. Heero went to Libra, without a mobile suit to see her.

5. In the Japanese version of Endless Waltz, Duo comments that Heero would do anything for a crush, when Heero mentions that Relena was kidnapped.

6. Relena never stopped believing that Heero was alive after he self-detonated.

7. That look Relena had in her eyes when Heero came to the Sanq Kingdom.

8. He gave her a teddy bear.

9. Heero promised to protect her. He never had to, and face it Heero's problems would probably be less if he didn't promise to protect her.