Just thought I'd throw this out there since the consensus is that Atmel Studio is getting slower and slower.
I've been pretty frustrated with Atmel Studio 6.2's performance (6.2.1563 - SP2). The issues that affected me across 3 different Windows 7 computers were in the areas of startup and doing simple things like reconfiguring project toolchain/devices. To just look at my project's properties, it takes about 75 seconds of unresponsiveness. Switching tabs also takes about 40-75 seconds too.
The fix was darn simple, uninstall Atmel Software Framework from your computer's "Programs and Features"!
Now opening project properties is down to seconds, and switching 'Tabs' in the project no longer freezes up.
It's actually a pretty decent tool now that it's not irritating the heck out of me with unresponsiveness.