I looked at the Advisor download page, but it doesn't go into details about how it gathers data. Is it a static inspection of the DB and the code stored therein, or does it watch the real-time SQL statement flow a la the Profiler? Most of our reporting queries are sent by external code in MS Access and Visual Basic.
Actually, you can run your own profiler trace which can be imported into the Upgrade Advisor. However, the Upgrade Advisor does not run the trace for you.