What do you mean, needlessly confusing? The release order was genius. Opening with the movie screening showed exactly the kind of show it was. It also allowed the climax to be in the last episode of the season, while still having it happen in the middle chronologically (as Haruhi wanted).
But the second season was where KyoAni outdid themselves. It was an improvement on the first season. While the first season was great, the second was even better. Sometimes you see a series dip in quality in S2, but here it was the opposite - the quality improved. For the second season showed an uptick in the narrative. The first season had already pushed the limits of storytelling, but the second went further. While the first season was greatly enjoyable, the second was even more so. Perhaps the most ardent fans may try to quantify the quality, and say that it was, I don’t know, eight times better than the first.