Best of both worlds
I guess a lot have people haven't heard of
A lot of the philosophies behind this apply to this debate, and can be adapted to RPMs, DEBs, or whatever. Basically, apps are installed to application directories (say in /usr/local) and
get symlinks in the official areas pointing to binaries, libs, mans, ...etc in the application directory.
That way, If you wish to manually delete something you can
just delete the application directory and run a program that
cleans up broken symlinks.
The only thing the author brings up that this doesn't address
is the non-root install thing, since other users won't have
rights to create the symlinks.
...Just my 50th of a dollar.