Have you tried both? Both brands, that is?
To me Atomics have a very different feel than Fischers, always have. I use Fischer RC4 WC GS (race stock) as my everyday ski and used to race on Fischers in college. Me likes my Fischers. I slay the NASTAR course with 'em.
One difference is the plate: Fischer plates will accept any binding; Atomic plates are proprietary.
Both skis are fine skis, to be sure. You should really try to demo them, or demo similar skis in each line (like the FIS-sidecut GS skis) just to compare the *feel* of each. From both, you'll get superior edgegrip and great responsiveness. I tend to think of Fischers as being more stable and torsionally stiffer than Atomics. My friend the zealous Atomic missionary swears that his edgegrip is better as well the quickness edge-to-edge. When I compare their GS skis (FIS legal), I think the Fischers get better with speed--rock steady on edge--and I can flex the Atomics into tighter turns easier than I'd like to, even at slower speeds. But that has more to do with how I ski and my height/weight on that ski length for GS skis.
When you're talking about skis at this level, you really need to feel the difference yourself. Given the same length and sidecut, they will both be exceptionally competent and hold whatever line you put them on through the gates. The differences will be in *your personal preferences*.
But I'd say get the Fischers