Will homebrew switch the default install location out of /usr/local for new installations then? I doubt most developers will want to dive into recovery mode just to install wget.
The only problem is that its owner gets reset to root on every OS update, whereas Homebrew wants its owner to be the Homebrew user.
The advantage of /usr/local as the installation root is that /usr/local/bin is in the default PATH of the OS and that setting the PATH in a way that it takes effect no matter what starts an application is a bit... tricky in OSX as there are many ways to launch an application that doesn't go through a shell, so .profile and friends aren't enough.
Or you don't chown and run brew as root.