I've thought about that too... actually, i've been wanting to try an architecture where we don't have: /var/lib/pacman/*/foo-1.2-1/desc but /var/lib/pacman/*/foo-1.2-1 as a normal file, containing all info. Less files == good.
Still, part of the reason the pacman3 DB format hasn't changed much is for easy of transition. I don't feel comfortable saying "run this script to convert your DB" or something like that.... so basically it needs to be thought out well in advance.
I think that is a reasonable position though. I think holding to backwards compatibility in *some cases*, will only maintain previous limitations. I think the major version change (pacman 3.x) is a good indicator to end users that things like this are expected to change.