Well ... having a cache pruning mechanism is on my wish-list, but the fact that it's not there yet is because it isn't necessarily easy if you use page caching component (most of the times a plugin such as wp super cache or alternatively a caching reverse proxy such as varnish) to accompany Autoptimize, which I consider the default setup. In that case the aggregated CSS/JS should remain available for at least the time the pages are in the page cache (because otherwise requests for Autoptimized CSS/JS results in 404 errors).
The reason for a cache size that grows to big in general is the fact that your pages have code (in general JS) that varies with every page (e.g. a unique ID per page used by an affiliate marketing plugin, see this thread for an example). Excluding that JS from being aggregated will drastically limit your cache size, to the extend that cache pruning becomes a nice to have instead of a hard requirement.
Hope this helps,
frank