ikiwiki could have an option to process /etc/ikiwiki/wikilist and run ikiwiki in aggregate mode for all wikis that need it. The Debian package could then include an optional cron job to automatically handle aggregation.
You can actually use ikiwiki-mass-rebuild for this. Just pass --aggregate --refresh to it. (The program could have a clearer name, perhaps I should rename it to mass-ikiwiki? ikiwiki-map? ikiwiki-all? ...)
A cron job like the one you suggest could also handle cases when plugins call for a page to be rebuilt. For example, a calendar plugin could use this to refresh a calendar daily.
I do worry that such a cron job would produce more load than might be optimal. If you have one wiki that never needs to updated, another that might want to update daily, and a third that wants to update every 15 minutes for aggregation, updating all three every 15 minutes wastes a bit of CPU time. Two cron jobs seem like a better fit in this situation, rather than a one size fits all master cron job. But it would be fine adding a cron job as an example, at least.
Another problem is that ikiwiki --aggregate will fail on any wikis that don't have the aggregate plugin enabled. This is really a problem with the plugin's special-casey approach of adding a new flag. This could be fixed by adding a more general syntax like "--set aggregate=1". (done)
Sorry for making this sound so complex, it's a good idea, but I'm on an airplane and have nothing good to do except blather on here, and read haskell tutorials. --Joey