I seem to be one of the only people around who actually liked Shannon and Sayid together. I got to thinking about this after reading a posting online and here are my loosely constructed ideas on them...
I think that Shannon was a major part of Sayid's redemption arc.
My view of the Sayid/Nadia relationship was that in Sayid's mind he thought that if he could love her somehow he would be making up for his flawed past, that if he could shelter her that he was somehow redeeming himself.
It was only when he let go of that idea, let go of Nadia that he opened himself up to truly love. And though Shannon was also flawed I think that they needed each other. She didn't feel good enough either and was chasing after all of the wrong sorts of men. While brief I believe that their relationship was the most significant of either of their lives.
Also when Sayid made that deal with MIB and talked about the woman he loved who died in his arms, I totally thought right away that he was talking about Shannon,not Nadia. He had finally let go of the chase for redemption in Nadia. That is also why Nadia was part of his FST world. He had to be willing to let her go in order to "move on" just as he had in the original time line. That is why it was Shannon and not Nadia that "woke" him up.