The producers had a relatively important challenge to overcome in this episode. The pilot was enormously expensive, and the budget was well beyond what a normal television series could hope to sustain. The typical victims of budget constraint are production quality and scope. (Fans of shows like "Supernatural" know this all too well.)
The good news is that this episode made me forget about the quality control concerns. I didn't notice too much of a dropoff, and the confines of the story made the lessened scope logical. In effect, it was a second pilot. The true pilot set up the character dynamic and most of the mysteries, while this episode demonstrated how all of that could apply to more episodic material. I think the concerns have been laid to rest.
Not all is perfect in the world of "Fringe", however. The characters are still settling into their roles, and while the transition is relatively smooth (since the same writers were involved from the pilot), there are some subtle tweaks. Walter Bishop's insanity is shining through a lot more than in the pilot, for example. This is not particularly bad, since his insanity brings a refreshing "mad scientist" atmosphere to the series, but it is a noticeable adjustment.
Oddly enough, the gore factor did not bother me quite as much as I thought it would. I tend to avoid procedurals and medical dramas when they use excessively graphic scenes to appear "edgy". In this case, however, we're mainly looking at situations well outside the norm. It's contextually relevant to this particular series, so perhaps that makes it easier to bear.
I like the complexity of the mythology that has emerged in so short a time. All that we know, and all that Agent Dunham knows, is that Dr. Bishop's old research has been twisted into something horrific called The Pattern. Someone or something may be behind it, and Massive Dynamic is not above using the same technology. It may be that Massive Dynamic is the true enemy, and their activities with Boyles' alliance against the Pattern is just a matter of keeping enemies closer. (I'm almost positive I missed some of the subtleties.)
The mystery itself was quite interesting, especially the possible ties to Peter. It was a good decision to connect one of Dunham's old cases to something within the "fringe" world she now inhabits. It touches on the classic Abrams premise of the "world underneath", and the notion that the FBI is becoming obsolete in a world where the real threats are unseen, even by them. It makes sense for those cases, the ones with a frightening new layer of reality, would begin Dunham's education.