Ability to exclude sub-tasks from board data sources

I want to use boards as data sources for convenience and to get the velocity info for the associated teams.  However, since the board filters show sub-tasks, once I add 7-8 boards to the plan, it gets very slow and can go over the 5000 issue limit.  Sub-tasks aren't relevant for planning at the portfolio level.  Some suggestions:

1. Just give an option to exclude sub-tasks, OR
2. Make a way to add a JQL filter to the data sources to exclude certain things that would otherwise be included (sub-tasks, very old issues, etc.).

I can't find a workaround for this.  If I just based the plan off JQL, then the teams' correct velocity isn't shown.