Having now performed both and upgrade and a fresh install of 126.96.36.199 and compared the two I can report that the upgrade does not entirely work - it seems to miss off or not completely install some components.
I'd already mentioned that the Essbase components were not included in the upgrade and this is perfectly ok - you'd want to install Essbase in a seperate middleware home anyway (if not a separate server), however some other new features don't seem to work after the upgrade and I can only assume the upgrade process doesn't install the components correctly.
An example is the new percentage tiles. the upgraded version doesn't have the correct screen when editing percentage tiles - it tries to edit them in the pivot table editor and it doesn't quite work properly - there isn't even any 'done/revert' buttons to save/discard your changes.
I also had a problem with drilling not working - clicking on a dimension value to drill down in a pivot table didn't do anything - even on a report which worked perfectly ok before the upgrade. This may be a problem specific to my environment, I've no way of knowing, but I don't have time to investigate it.
I'm going to keep my upgraded environment (it was only a test environment) and when the next patch set comes out see if that fixes these issues - upgrading would still be an easier option than reinstalling especially if there were lots of custom configurations. For now though if anyone wants to upgrade I'd recommend a re-install.