The 100MB per domain includes the subdomain storage? Then it doesn't solve what parent comment described - few subdomains could use up all the storage. If it doesn't include it and it's separate then it is exactly like it is now.
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.