[eluser]kanjimaster[/eluser]
We host most of our clients' sites so have a directory near each server's root with each version of CodeIgniter. We then point each client's site to this folder via the index.php file.
This way each time there's a new version of CodeIgniter we need only upload the new version once per server, and then update each site's index.php to use it.
The updates of the index.php files could be automated via a script, though in practise we haven't as it's still a good idea to do some level of regression testing to ensure that the upgrade hasn't upset anything.
We also use HMVC to modularise each site very aggressively and then reuse those modules on other sites, which substantially reduces the total amount of regression testing due.
My recommendation too is that you don't think in isolation about the extra time to spent upgrading. It's very small compared to the amount of time you'll save on developing sites in the first place.
