Now that it's clear that the Swan Station is under construction, it seems a given that "the incident" mentioned in the Swan Station orientation film will be taking place sooner rather than later. The death of Alverez appears to tie into the claim that the electromagnetic anomaly is highly variable and potentially lethal. It's already clear from Desmond's experiences that the electromagnetic and time anomalies are tied together in some way, despite the physical distance between the Swan and Orchid stations.
One interesting aspect to this episode is that it adds to the growing depth given to the Dharma Initiative. While the Dharma Initiative was quite mysterious at one point, they were almost always depicted as the innocents. The Others were always the menacing evil. This season has revealed the darker side to the Dharma Initiative. While the reasons for the initiation of the war between Dharma and the Others is still unclear, and it's still not known who ordered the Purge, but it's clear that Horace and his inner circle were a lot more scheming than originally thought.
The end of the episode would appear to answer the question of where Daniel was all this time. The reference to Ann Arbor ties him to the home base of the Dharma Initiative, where the DeGroots would have presumably been all this time. It would be very interesting to know whether or not he was interacting with his mother at all, or if he was involved in working at that station under the church at some point. At any rate, this might explain why he can sneak onto the site for the Orchid eventually, as seen in "Because You Left".
All of which simply proves what is already known about "Lost": even a simple transitional episode is full of hidden gems to consider.