Tried to do an in-place upgrade as above on a production server on 12/3/2016 with a slipstreamed 2008 R2 Standard installer, but only the Setup support and SQL Writer were updated. A similar upgrade on a test server on 11/17/2016 with the same installer worked flawlessly and upgraded all features. Both servers only have/had a single default instance of SQL Server 2005.
From what I can decipher from the logs for each attempt, it appears the production server upgrade did not have an instance id specified in the generated configuration file when it got to the rules evaluation, even though it appears to have detected all of the installed components and the existing instance correctly. The upgrade screen on the production server also only presented a grayed out incomplete Feature List.
Would appreciate any feedback on what caused this, and how I can get the upgrade on the production server to process correctly.