My main reason was, since 2.0 doesn't include a "run every X minutes" option, I figured it might be easier to make it very minorly scriptable so I could manually make it run on specified intervals. Also, being able to have each folder's rules run on different intervals would be awesome (some of my folders only need to be acted upon once a day anyways), and since the menubar access allows that, it'd be cool if it was accessible via applescript.
The memory usage of hazel 2.0 is a lot more than 1.0 so far, and I'm trying to cut down on background app memory usage, so that's the main reason I'd like to make it run a little less frequently.