Writing the conditional activities code so that it uses conditional plugins.
The administrator would have the ability to turn on/off which conditional plugins can be used throughout the site. Just like the other Moodle plugins, such as the enrolment plugins. This would allow developers to write their own plugins and share with the community without hacking core code.
There has been a lot of interest with this since the introduction of conditional activities in 2.0. People want to go beyond restricting via grade, and have restrictions based on user profile fields (http://tracker.moodle.org/browse/MDL-29538), groups (http://tracker.moodle.org/browse/MDL-30554), cohorts, time spent in a course (apparently its not uncommon to have credit or certificate requirements based on a time standard along with the curriculum requirement) etc.