There's no question that the behavior changed. And clearly you do not
like it. But ... what's the harm?
Lots of programs create a ~/.foo directory at start.
Just a question: is the creation of this empty directory (~/.emacs.d) the
result of a design in the code for the next Emacs 23.2 or is it a unexpected
result of that code?
It's not on-purpose, no. It's not exactly unexpected, tho. The issue
is pretty simple: Emacs packages often can use either ~/.<foo> (old
style) or ~/.emacs.d/<foo> (new style) files to store some customization
or state.
If neither of the two files exist, we prefer to use ~/.emacs.d/<foo>,
but at the time we make this choice, we usually don't know yet whether
the file will be written, and at the time the file is written, we
generally assume that the parent directory already exists.
So the ~/.emacs.d directory is created eagerly.
In other words, this behavior is clearly not a feature, but "fixing" it
is somewhat of a pain for very little gain.