Well, this was certainly something. Essentially, it's a classic who's-the-mole storyline. The interesting thing is that you basically know who the mole is the entire time. The conflict comes from Chakotay's personal struggle to come to terms with it.
Chakotay was already betrayed by his crew once (with Tuvok), and here once more, something he notes. Seeing Chakotay, a man noted for his honor, having to deal with repeated betrayals of trust is an interesting dynamic. It's also rather funny, since the Maquis are supposedly the ones known for betraying the Federation and Starfleet, yet the only traitors we've seen so far have been traitors to the Maquis cause itself.
The development of the Kazon here is also rather interesting. They're a far less advanced race (blowing themselves up over a simple food replicator), but they're still a threat to Voyager merely through sheer numbers. It will be interesting to see how they further develop as a threat as time goes on.
With Seska's defection, on a personal and political level things just got a bit more complicated for Voyager.
