Apple TV: Only works with iTunes, limited to 160 gb drive (as opposed to 250gb in BM1), no fast scrolling from Beo4.
BeoMedia: Larger, x6 higher cost, incredibly limited video functionality, only works with BeoPort, functionality with Macs is pretty poor, difficult to set up, doesn't work with older sets, no ability to stream from a computer, no HD video playback, visually less appealing, only works on a B&O set, limited audio format playback.
That's all I could think of off the top of my head. I'm sure there are more things to consider...