I think it's a bit of both. I do think that Kishi wanted Sakura to reciprocate, but a post on Tumblr made me think that in the very beginning, he was considering the other pairings. Kakashi asked all of them what their goals were and thought that all of their answers were stupid. Naruto was at the time fairly immature and a terrible ninja according to his Academy days. Sasuke is purposely closing himself off in order to steep in feelings of hatred. Wow, what a great goal. Kakashi sees the issues with this. He narrows his eyes when he thinks 'like I thought.' Sakura glances at Sasuke and implies that she is interested in him. Kakashi remarks to himself that girls are more interested in love than ninjutsu.
There are problems with what all three of them have said. Naruto needs to shape up before he's ever considered, Sasuke's goal is going nowhere pleasant, and Sakura only has eyes for Sasuke. If Sakura had development like Naruto and Sasuke had with their goals, then I would have understood her ending. If she realized that she didn't understand Sasuke instead of just thinking that he's cool and then being able to interact with him and talk with him, then sure. It would have been a good pairing. And having all of them achieve their goals, but not in the way they envisioned them would have been a really cool thing to pull off.
Sakura was on the verge of being able to understand Sasuke at the end of Part 1, but he knocked her out and peaced out for a few years. Years that she spent training to help NARUTO because she realized how much Sasuke meant to NARUTO as well and that what she asked him to do for her was selfish because she made a mistake and only thought about her own feelings. Then we got a TON of development with NS because they are friends, they are on the same team, and they are both trying to go after Sasuke.
This is where NS pulls away in my mind. If Naruto had backed off on Sakura for whatever reason or interacted with Hinata before randomly getting thrown on a team with her for a couple chapters and Chapter 615, then NH would have been great. But it makes no sense with this ending.
At the end of Part 1, I think NS and SS had a somewhat equal chance. NH was laughable because Hinata had only ever given him ointment which he promptly offered to Sakura. (I felt so bad for her. You idiot Naruto. Read the atmosphere! lol)
After looking through what we know about Harry Potter after the fact, JK said that HarryxGinny/RonxHermione was her original plan, but admitted that the story did point a lot towards HarryxHermione. I didn't really ship HarryxHermione and I actually quite liked HermionexRon (I actually like them all as platonic friends tbh), but I was terribly confused when Harry got with Ginny all of the sudden after seeing her as first as Ron's shy little sister for a few years and then dating a few of his friends randomly. I'm not saying that this is bad, but I didn't think that Harry thought of her that way. If they'd had more interaction or worked together on things, then I wouldn't have scratched my head.
So before the beginning of Naruto, Kishi had a rough framework of where the story was going. Maybe he did hash out NH and SS, but when it came to what was needed for the story, NS ended up getting more screen time and therefore more development. I still think that NS was intended because of Chapter 3 (and the entire rest of the manga until chapter 698), but maybe he also had the others in mind as options and in his mind, there is infinitely more info on this world and off screen interactions. Who knows what kind of external forces also acted on the direction of the story?
Sakura was not a popular character from the get go because she was pretty much a bitchy teacher’s pet who was mean to our sympathetic main character. Naruto is a trouble maker brat, but from chapter 1, we got backstory on why. It took a long time before we ever got anything like that for Sakura (Chuunin Exam is the first time I think we see her introspect in a meaningful way) and I think her popularity has always suffered because of that.
I will say that I really do like relationships that start off as friends first. I don't really care for relationships where someone claims to be head over heels for someone that they don't have a close relationship with. How can someone love that person? (a.k.a. why I didn't originally ship NS before Sasuke told Sakura off about how he always does thing for her and looking back how he DOES understand some of her deeper feelings.)
This sort of slow build isn't popular with everyone because you have to be patient and wait for feelings to grow. When characters declare from the start who they like, it's much more succinct and you can start shipping right away.
tl;dr
Maybe SS and NH were considered alongside NS as possible in the beginning, but the pacing of Part 2 put NS way ahead and makes this SS/NH ending very bizarre.
I can only imagine too how everyone in Japan must feel about such a cop-out of an ending as well as how FORCED it was. 
) It's really a shame. And I agree with this post, because Kishi has been consistently being contradicting near the end of this series. I honestly am not surprised anymore, but I won't stop being disappointed. I'm wondering Kishi himself is happy with what he's done with his manga. I doubt it. He probably just left it on the note he did, so he wouldn't have to deal with it anymore.
