Just my 2 cents.
Very good idea!
I would use a base inspired from BetterWb because it's a very fast and light distribution, then add all the good visual enhancement from MagicWb because it has set a standard, very recognisable, and neat, of our beloved Amigas. MUI of course too.
I'm not sure OS3.9 is even a base to be considered, as OS3.1 does already everything and can be enhanced. Not to mention OS4 which requires exclusive Amiga classic.
I'm very interested in your project because I have all sort of issues with ClassicWb, to begin with: the localisation... Never been able to have a proper French on my Wb with this package...
Other than that (and again, just my own and humble opinion) I would stay away from too big graphical stuff which would compete with AmiKit for real Amiga which does it very well.
All the best, I will follow this thread... Thumb up!
...Ah, also creating a front-end to chose what to install and what not to install would be great (commodities, drivers...).
...And all that installable from WinUAE to prepare CF cards quickly before to install them in real machines.