This really isn't that hard of a problem – allow X MB per domain and Y per sub-domain (user configurable or set by the browser developer to some sane limit – the actual number doesn't matter too much within certain ranges, in reality).

After either of those limits is hit, prompt the user to grant another increment of allowed storage or a customized amount, possibly (and disclose how much each domain and subdomain is using under a detailed view option). In the end, this puts the power back in the hands of the user and prevents any malicious usage while not allowing one subdomain to effectively deny storage to others, etc.

Yes, it would be 20 subdomains though, and the user would get a prompt for more storage allowance.