To be quite honest marco there wasn't a really painless way to update major changes as mentioned before to peter; not with my limited free time and average install script writing ability anyway.
To tell you the truth it should no longer pose a problem to anyone very soon. I've considered this for a long time and decided the next release is going to be the final version in terms of major changes.
The only future updates will be those programs still actively developed for Workbench 3.0/1 which are WHDload and SFS. These are easy to install incrementally, so will come in the form of an update pack which can be applied easily (I'll add an update option to the tools menu).
Why? Well, most new software is designed for OS3.5+ so there is nothing major to update or change. The FBlit/Ftext and pure workbench boot were really the last major things I had in mind for the ClassicWB which has been updated for over 5 years!
I don't think there will ever be a new non-beta Scalos release as development, testing and interest is very low (and seems targeted at OS 3.5+ now). I've now put in place everything I possibly want, with the exception of OS3.5/PNG icon support which is really slow and pointless on most classic machines anyway - newicons are fine for that.
So fear no longer - the next packs will be the final versions that require a major re-install.