Okay, it's been an incredibly long time since I've thought about or discussed Naruto at any depth, but let me give this a shot.
First of all, there are definitely more than just a few examples of their connection clearly being fleshed out. You have their formal introductions to one another, Sasuke empathizing with Naruto when Sakura did not, and Sasuke also revealing his softer side when he decided to share food with Naruto. During the Wave Arc or whatever it was called (Zabuza, Haku, etc.), they trained together, and helped each other out (cute scene I remember: Naruto having to lean on Sasuke after their all-night training session). Against Haku, both invested a lot into protecting each other.
The Chuunin Exam Arc had a few big moments for the SasukexNaruto connection. Aside from all the additional time spent helping each other through dangerous situations, there was the time when Sasuke acknowledged Naruto as a rival, and the time (vs. Gaara) when he acknowledged him as a precious person, telling him to run away because he didn't want to see another person precious to him die. Skipping ahead, during Sasuke's whole inferiority complex ordeal (before he bounced from Konoha, as I believe the city was called), it was made very clear that he viewed Naruto as family.
So there was build up - the emotional aspect behind the Sasuke vs. Naruto fight didn't come from nowhere. Now, all that said, to some extent it was unearned. In a number of ways, their relationship wasn't especially fleshed out, and at the very least the fight presented a fairly sudden tonal change to it.
That tonal change, though, also pointed to a couple narrative points. Sasuke and Naruto were never totally open about their feelings for one another, and the fight was specifically the platform where they acknowledged the special roles they occupied in each other's lives. It's obvious they hadn't been mere rivals for a very long time; their developing rivalry also reflected their developing connection overall. Additionally, the fight was where we started to learn how their lives were intertwined on a grander scale (their not totally dissimilar pasts drawing them to one another much earlier on, Sasuke always being Naruto's reference point, the sense of destiny portrayed by the statues they fought around, etc.).
So, again, there were definitely issues there, but it worked for me overall. I'll always remember reading the chapter where Naruto caught up to Sasuke for the first time, and how much atmosphere was infused into those panels. As erratically written as a good amount of the stuff surrounding the fight was, I was pretty invested in their friendship by the end.
Part 2 is when it all becomes unadulterated garbage.
