The ability to get GP to run a check links and reconcile automatically via a schedule would transform the admin of larger sites.
I would love to reconcile our SOP and POP each night and IV over weekends, automatically and have the resulting reports written to a directory for me to review. Even if it meant passing params to GP application via windows scheduler or having another application to run on the server. Alternatively hooks into these processes for GP Addin would help.
This is a hidden pain of GP admin currently.
This also relates but not depends on another suggestion, of moving the reconcile and check links into SQL for easier management.