Your proposals (taken as a whole) are fine for particular circumstances but not as defaults on a general purpose OS. Someone obtaining Debian may be doing so to create a home desktop, a cluster, a web server, almost anything. So in terms of file system hierarchy and user and root privileges they get a quite generic system by default. This is fine as it is for many purposes but serves as only the starting point for others. Your proposed configuration would suit only a few circumstances easily but in general it would be an unwelcome set of defaults. This is especially true for new or less experienced users/admins who would have acute
difficulties in administering and using such a system. It would also be true for anyone running a testing or unstable release and for many doing development. It could turn simple tasks into a serious of tiny annoying obstacles. For people running a stable release, especially those administering it remotely, it could be quite annoying to not get automatic package management update of cache, downloading and installation of security updates and instead have to log in and remount / and do it all themselves. It would mean that before doing a simple apt-cache search one may need to remount filesystems to be sure one is seeing an up to date result.
One thing I noticed on your website was
A mistake made by many distributions is putting package manager's state files in /var. In fact, these state files only change when packages are installed or uninstalled, so they are not any more "variable data" than files contained in packages.
But this isn't exactly the case. The package manager needs to write to disk not only when installing/uninstalling but also when updating, so if package management can't write this does a nice job of disabling it in a fundamental way and completely precludes automation.
I don't mean to criticise because I like your ideas but I don't think they are right for a general purpose distribution.