One problem I often run into is that the Django libraries expect the whole application to be run by something that uses manage.py, which sets particular os.environ settings. So if you make code dependent on a Django library, often it cannot be run any more by non Django code. The eventual result is that things like cron jobs and unit testing are second-class citizens.

Another problem is unicode. Current Django assumes you will deal with all strings as valid unicode, which is actually different from pre-1.0 Django. There is no way to store an arbitrary sequence of bytes without a unicode encoding. This makes perfect sense for a newspaper website, but is problematic for many other applications.

Another problem is imports in general. Django does a lot of work in __init__.py files which causes problems integrating it with other systems that do a lot of things at run time.

The article gave some examples that I've run into myself: using email addresses instead of usernames for authentication, and adding additional fields to the User class. I also dislike the template language. Why invent your own language and control structures when everyone using it knows python? Mako (http://www.makotemplates.org/) does a good job of not reinventing the wheel.