There was one very useful contributed module named Hosting Advanced Cron. It allowed me to set cron interval per site, instead of set just global for all (and you can even disable cron on specific sites). hosting advanced cron
For Aegir 3, there is no such release and development seemed to be stopped. There is a fork on Github by omega8cc, but it is not functional (doesn't work, has error and notice, has debug statements left on), so does anyone have a solution or a replacement for such a useful feature for Aegir 3?