For quite some time, the Debian version of WordPress has had a configuration tweak that made it possible to run multiple websites on the same server. This came from a while ago when multi-site wasn’t available. While a useful feature, it does make the initial setup of WordPress for simple sites more complicated.
I’m looking at changing the Debian package slightly so that for a single-site use it Just Works. I have also looked into the way WordPress handles the content, especially themes and plugins, to see if there is a way of updating them through the website itself. This probably won’t suit everyone but I think its a better default.