I've never thought much of the "Gormogon" arc, it seemed stuck on as an afterthought, a plot device to give Hodgins something to point to gleefully. So except where it was the primary focus of an episode, I've mostly ignored it.
What I HAVE paid attention to over the three seasons has been characterization. The "squints" are a well-working machine, a team made up of individuals who nevertheless add up to more than just their numbers.
Hell with this. If you're into the show, you know what I'm talking about; if you aren't, you'll probably not give a damn. Suffice to say that, up until now, Bones hasn't violated its characters for the sake of a silly sub-plot.
I'm going off on a bit of a tangent here to illustrate my point, so bear with me. I'm a big fan of Thomas Harris, especially _The Red Dragon_ and _Silence of the Lambs_. I liked the character development, especially the interesting - and adversarial - relationship between Lector and Starling. So, when the third novel, _Hannibal_, came out, I was excited and bought it before it was remaindered in hardcover or went into paperback.
BIG mistake. The final scene, with Starling and Lector having a romantic dinner of her ex-boss's brains while he was still alive, utterly repudiated the character of Clarice Starling as Harris had spent an entire novel building, and didn't treat Lector with much authorial respect, either. It's the closest I've ever come to actually throwing a book across the room.
Much the same here. Zack Addy has been an integral part of the Bones machine since the beginning. He's been through some changes, which is part of being part of an on-going story, but he's been quite the steadiest of the squints, reliable, clever, and clearly the only one there whose intellect is the equal of Temperance's.
(Let's leave aside for the moment that in the last episode, Booth took a hit to the chest, yet in the bath-tub scene shows neither wound nor bruising, which would have been present even had he been wearing a vest. That's the least of the problems with this episode.)
There was absolutely no overwhelming - or just plain whelming, for that matter - reason for Zack Addy to be the Apprentice. It was a stupid choice, all head and no heart. Zack Addy, as he has been depicted in the show to this point, simple would NOT have fallen for some charismatic yobbo with bad eating habits. I cannot imagine the justification he could have given himself, let alone what he'd tell his friends once they found out (and it was inevitable that they would), and the writers and producers must have felt the same way, because WE'RE NEVER GIVEN ONE.
It's as if somebody said, "Say, who's the least likely candidate in the Bones continuity to be Gormogon's Apprentice? Zack? Okay, what the hell. Let's give it a whirl." All head; no thought at all about the violation of Zack's character. None.
It was bad writing, it was a silly and stupid concept. It wasn't a surprise, it was a bewilderment, a cipher. The only possible way for them to preserve what had been to now a really rich and fertile source of character-driven stories would be for the first episode of the fourth series to begin with Temperance waking up in bed and saying "Oh, God, what a terrible nightmare." I have no confidence this will happen; at this point, I have little confidence in the show at all.