The whole ending was Shahra losing the man she loved, who also abused and used her until the very end. Nothing can make it better, nothing can bring him back, so Sonic did the only thing he could do: provide some sort of comfort for his grieving friend because there's nothing else he *can* do

The scene hits different 17 years later I guess, especially since I was 13 at the time and hated the game due to the controls compared to being almost 31 and having gone through something similar to her.