I was having the same issue - couldn't believe my eyes on how horrible and fuzzy Flash Builder looked on my new Macbook Pro w Retina. Was suffering through it for the past week and just found this work around that someone figured out for Eclipse that also works on Flash Builder (guess b/c it's built on Eclipse). Here's the link to the bug report that shows the work around (Thanks to Brad Hudgeons):
here's a cut and paste from the bug report in case the above url gets removed:
Here's the workaround: Do "Show package contents" on the Eclipse.app. Edit Contents/Info.plist. Just above </dict> </plist> Place this: <key>NSHighResolutionCapable</key> <true/>
Instead of Eclipse, show package contents on Adobe Flash Builder 4.6.app. After you edit the Info.plist file, go back up to the Adobe Flash Builder 4.6.app and duplicate it. It will create a Adobe Flash Builder 4.6 copy.app. Delete your original Adobe Flash Builder 4.6 and rename the Adobe Flash Builder 4.6 copy.app to Adobe Flash Builder 4.6.app. Then launch Flash Builder - you should see text that is much clearer. The graphics on the ui are still blurry but at least the text should be crisp.