I had some big performance problems after installing Lion with Aperture 3. I noticed also that this was reported on the Apple support blogs and elsewhere. My fix was a re-install of Lion which I ran overnight.
After the second install all of the performance and memory leak type problems went way. Longer description of fix here:
Posted in case anyone else affected.
I too experienced issues in Aperture 3 after the Lion upgrade. My problem ended up being video files that were mixed in with certain libraries in Aperture. This took days of trouble shooting but once I located and removed all 36 video clips from the Aperture library all was perfectly fine. I was able to boot Aperture while holding the Shift key and did not experience the issue, this led me to the video files as a potential culprit. I did not reinstall Lion and so far Aperture is working perfectly (without any videos).
Hope tis helps someone.