MySQL is still working on the problems regarding the incompatibilities. In the bug reports there are some advices which will be released in the next release I guess. If you can’t wait, here are the solutions:

The not working preference pane has an update which you can download from here.

The issue of not starting up properly has to do with the user rights on the data directory. You can change them to the proper user by the command:

chown -R mysql:wheel /usr/local/mysql/data

Hopefully the next release will address all the issues. If ou want to read the bugreport yourself you can do that here: http://bugs.mysql.com/bug.php?id=28854