Well, it mostly makes sense. The one area that I still have a little trouble with is that he was unwilling to bend far enough to at least send a message, or acknowledge their existence, in "Letters From Pegasus". It's just a little odd, is all, because from what we saw of his brother in "Outcast", he seems like a decent enough guy -- certainly not the sort to inspire the level of animosity towards his family that John must have felt to have basically had them be "dead to him" for years. Especially since he's so devoted to his Atlantis "family"; it's just an interesting contrast.

But I don't mean this to sound like I'm criticizing him, because honestly, it's John's flaws that draw me to him -- and to know that he's capable of being stiff-necked and irrational and carrying grudges is actually a point in his favor, in my book. I feel like we've really gotten to know the character a lot better this season, his strengths and his weaknesses, and I really love that.

And it also says a lot about how much he's changed through the course of the series that he's willing to seek reconciliation with his family in season 4, where he wasn't willing to do the same in season 1.