I just had the same problem on two different Macs. I phoned AppleCare.
They know about the bug. They believe it impacts people who previously used MobileMe with Aperture (I did). My other half didn't have the upgrade problem, but my other half also didn't use Aperture with MobileMe.
I was fearful that, since it said a library upgrade was required, that it damaged my library. Turns out the library upgrade was fine and all photos were fine. The issue is a .plist file corruption, but that's very easy to fix.
The fix is:
Close all apps.
Open Finder.
Hold the "alt" key on the keyboard and click the "Go" pull-down menu (in finder) which causes the "Library" folder to appear (the "Library" folder wont be in the list if you aren't holding down "alt".)
Pick the "Library" folder.
Navigate to the "Preferences" sub-folder (under Library)
Find the file named "com.apple.Aperture.plist" and drag it to the Desktop (you can drag it anywhere as loing as you get it out of the ~/Library/Preferences folder.
ALSO... if you have a "com.apple.Aperture.plist.lockfile" (and you probably will) then you need to drag that file out of the Preferences folder (e.g. drag it to the Desktop) as well.
NOW start Aperture.
You'll probably get a message that the last time you tried to run it, it kept crashing. Just click continue.
Since you've moved the preferences file, you will get a few prompts that you're not used to seeing (I think you get a screen offering to give you an overview/tutorial, you'll be asked if you want to use it when a camera is connected to the Mac, and you'll get a prompt asking if you want it to show you were photos were taken on a map (which requires an interaction with Apple which would send the GPS coordinates of all your photos to them.) Aperture will create a fresh .plist file (non-corrupt.)
After that, Aperture will work normally again.
Once you've verified that Aperture is working, you can delete the copy of the old (corrupt) .plist files that you sent to your desktop. Just drag them to the trash.