Since migrating to 3.0 I have yet to see something like easy mod that was around for the 2.0 versions. What methods have others used to upgrade to 3.01 with the lack of a automated method. From what I can tell it seems the manual method is about the only way to go on a site with some mods.
A auto mod installer such as easy mod is in development for phpBB3 however I fail to see why you claim there is not automatic update procedure for phpBB3 when when of the update packages is called...and I quote
[ Automatic Update Packages (0/1-RC1 to 3.0.1) ]
This is a method of updating which will apply changes to the files automatically and only need human intervention if conflicts are found in the same way easymod would have when installing some mods
Custom theme and multiple mods im sure will run havoc with the auto updater. Easy mod was nice as it would show you what it could or could not update prior to doing anything. This allowed you to work through any issues before changing anything and quickly identified any mod conflicts.