It's not just you, I moved on to fanboying over other shows a while back and I felt this episode was significantly better than the first two.
As for trying to figure out why it's such a big improvement, I'd three two points:
1) More scenic locals: I initially went into Kanon 2006 not expecting much, and one thing that attracted me right of the bat was just how pretty that snowy town was. This wasn't on that level, but the new scenery was a big step up from the prior episodes.
2) Ensemble cast: I don't find Noel or Yuzuki interesting enough at this point to carry entire episodes, which is more or less what they were asked to do in the first couple episodes. The ensemble and its internal conflicts, on the other hand, is interesting to me.
3) I'll also note that I think Sora no Method tried to hit the emotional buttons way too early, before I actually cared about the characters. Kanon 2006 took a few episodes to introduce characters - rotating through them in the process - before it expected you to care all that much. Before that it was mainly comedy - and KyoAni more or less hit on gold with having Sugita inject a bit of Kyon into Yuuichi (seriously, in what I've seen in the 2002 version he's kind of a wet noodle). Sola admittedly got down to business much quicker, but early on it was going for tension, not emotion.
In retrospect, I supposed the fact Hokuto completely loses her nerves the first time she encounters him for no apparent reason in the flashback should have been a dead giveaway, but hindsight is always 20/20.
Well, yeah - until I knew Hokuto was origami I didn't suspect, obviously. But I thought as soon as that was revealed that Natsume was probably the one behind it - keeping tabs on Nanoha- er, Harutora from a distance...
Depending how far back you mean by "all along" that actually helps explain a lot about our wildly different opinions of Natsume - I found the layer by layer building of her personality rather endearing.
I'd probably pinpoint Hokuto's death as the point where savvy fans would pick up on it. Prior to that and I'm seriously impressed.
Golden Time and Naki no Asukara had good episode this week IMO though I felt really sorry for Chinami at times.