Every time there is an update, I have to go through the whole "setup" process once again (Next > Next > Next > Finish). This is a PITA for those of us who have auto-update notifications enabled and want it to be enabled (to ensure we have the latest and greatest SourceTree version ever!).

Usually, most software will only require you to go through the set-up process once on the first ever install (or when installing again after an uninstall). Updates happen seamlessly from then on, with minimal or no user intervention. I believe you can also achieve this by adding a silent option to the installer, which can be called by the updater. With the silent option, the installer would perform all steps automatically in the background, simply reporting progress to the updater.

Minimal intervention: An update is available. Would you like to download and install it? [Yes] Downloading... Installing... Installed! Restarting SourceTree... Enjoy!

No user intervention: An update has been downloaded, and will be installed the next time you start SourceTree. To install now, [Restart SourceTree].