When doing an install of upgrade there is a large pause at the end of the process which appears to be the last plugin bit its actually churning rebuilding the admin tree and looking for settings to be set to their default values.
Proposing two things:
1) improve the output so its more clear what it is doing
2) Look into ways it could be faster. As a baseline if I hack the upgrade script so its does an 'empty' upgrade then its takes 18 seconds to rescan purge, rebuild (10 seconds) and search (8 seconds) the admin tree for a total of 22 seconds. I have a theory that the searching step could be much faster because its normally cached but isn't because MUC is disabled here and it could benefit from a temp static cache.