That is the biggest difference... and also the most obvious and expected. The atmosphere responds far more quickly to any impact than the surface. Hence, when you plot graphs that are normalized to the same baseline, what stands out is the larger swings in atmospheric temperatures.
What is of major interest, over, is a comparison of the trend. Theoretically, we should expect a larger trend in the atmosphere, up until fairly high in the troposphere, where the trends reverse again. Note that this is entirely independent of greenhouse effects; it is a general question about the physics of the atmosphere for ANY prolonged temperature change.
That is.... for an increase in the mean temperature at the surface by 0.1C, you expect more like 0.12 or 0.15C increase in the mean at the atmosphere. You cannot see this until you abstract AWAY from the short term variation. The UAH group records smaller trends in the atmosphere... especially in the tropics. The RSS group records a larger trend. And the radiosondes lie somewhere in between; although they have errors of their own.
Unfortunately, the woodfortrees pages don't let you calculate trends as easily as one would like, and you can't look at particular zones... the difference is greatest in the tropics. The first graph with trend lines for rss and uah does show the guts of the problem, however.
Cheers -- sylas