The hook_cron_alter(&$hooks) allows you to change the cron hooks defined by hook_cron() and hook_cronapi().

Example

Change default rules for the Node modules cron hook and hi-jack system cron:

function hook_cron_alter(&$hooks) {
  $hooks['node_cron']['settings']['rules'] = array('0 * * * *');
  $hooks['system_cron']['module'] = 'mymodule';
  $hooks['system_cron']['callback'] = 'mymodule_new_system_cron';
  $hooks['system_cron']['file'] = drupal_get_path('module', 'mymodule') . '/mymodule.cron.inc';
}

Example of the Node modules cron hook data:

(
    [unsafe] =>
    [description] => Default cron handler
    [module] => node
    [configure] =>
    [settings] => Array
        (
            [enabled] => 1
            [rules] => Array
                (
                    [0] => * * * * *
                )

            [catch_up] => 300
        )

    [function] => node_cron
    [callback] => node_cron
)

Description of data structure

Name	Description
unsafe	If true, then the cron hook is considered unsafe, meaning that Ultimate Cron will not execute it. This value is set by Ultimate Cron when determining which hooks are unsafe. A hook is considered unsafe, if the function resides in a module with a weight lower than Ultimate Cron.
description	The description of the cron hook, usally defined in hook_cronapi(). The core modules description are added through a hook_cron_alter() in Ultimate Cron.
module	Name of the module in which the cron hook lives
configure	Link to module settings page
settings	Array with settings data, contains enabled, rules and catch_up by default, provided by Ultimate Cron
function	Name of function for the cron hook. Note: This is unsafe to change
callback	Name of callback to use when executing cron. This is set to the cron hooks function by default
file	Path to file (including filename) where callback is defined.