Seems like the AT vs SE argument boils down to how well the new hybrid system toe-strap is working out? The traditional straps speak for themselves but a review on REI says that the SE 2 strap system still needs improvements...
A buddy of mine bought a pair of SEs, because he really likes the idea of a toe strap. He's only tried it out once so far, and his major complain was not that the toe strap required improvement, but rather the fact that it slowed down the entire "quick entry" process.
He noted that almost every time he strapped in, a little bit of fidgeting was required to get the straps to sit where he wanted them. Once strapped in though he said they were very comfortable and responsive, with no pressure points.