I've been testing WP-Super-Cache on some larger wordpress installs and while it does work better than virtually any other wp caching plugin I've discovered one weakness:
On sites with a great deal of posts/pages, if you try to be efficient by having a very high expire time - it creates too many files for the cache pruning to work in realtime.
This causes very high loads and wait-times for admin users who are just trying to make or edit posts.
I'd like to modify this plugin so that the prune can be done by a real cron job or somehow spawn the prune as another php process - but I think the former is a better idea because if the pruning is done closer to the OS and not through PHP it will be faster with less load.
If anyone has any already done this or just suggestions in general please let me know, thank you.