Don't I feel silly. I finally got the chance to listen to both in the same room. The M3ti (these were not the SE's) were MUCH better overall. The M3ti's had a much clearer midrange and more natural sounding extreme highs. These seemed to dip a little lower in the bass too.
The Atoms could play louder without breaking up and had a warmer balance. But I felt like I was missing some top-end energy with the Atoms.
I'm buying a pair of M3ti's. I now know what all you people have been talking about.