I thought about this long and hard, and while all the pairings were a mess I'm going to have to say that SS was always the main pairing. My reasoning for this is that I honestly believe that Sasuke was always the main character of Naruto. Very early on in the series, during the Zabuza arc, I told my husband that this anime should be named Sasuke, because he was the strong one, he was the one that this anime was all about, and unfortunately my comment turned out to be true. Naruto is the one manga that has so little of the actual hero in it. I remember there were times when it seemed like forever since I had seen Naruto, especially during his training with Bee and the beginning of the war.
Now the way I see it is if Sasuke is the main character, then it would make sense that his pairing would be the focus,despite the fact that it was handled horribly,and that it's toxic. I mean its clear that he was never interested in Sakura, and when he did say how he felt it was reveled that he saw all of team 7 as family. However since Sasuke was indeed Kishi's favorite character I can see how it made sense to him to literally hand Sasuke Sakura as the gold trophy and then he gave Naruto the silver trophy. After all the hero deserves the heroine, and while we felt like that with NS, Kishi never felt that way about his own hero.
You look at the manga now and if it wasn't named Sasuke then it should have been called Uchiha. Their involvement, their infinite power ups, their amazing character Itachi, and then of course the one that it was all about Sasuke. It's clear that it was all about the Uchiha's, and it's because of that that Kishi felt Sasuke's feelings towards Sakura weren't important. All that mattered was that Sakura loved him. Just like Hinata's love is all that mattered when it came to Naruto. I always wondered why Hinata was added to the manga especially when she just disappeared after the time skip. Back then I had no doubt in my mind that NS would be canon, and Hinata just kinda seemed out of place. However looking back it's clear that she was added there as a back up plan for Naruto. I may not like Hinata, but even I think what happened to her in the end was a shame.
So with that said SS to me was always the main pairing. It fits perfectly with the rest of Sasuke's story. He was the one that never earned anything that he got. All his power ups were literally handed to him, and having Sakura in the end just wraps it up. Naruto on the other hand worked harder then anyone, things weren't always a walk in the park for him, but that didn't stop him. However when it comes to love he does indeed give up and settles. I don't think I'll ever understand how Kishi could destroy what his hero apparently stood for.