As far as I know, no one advocating abolishment of software patents sees the need for an alternative. Fat32 is not in common use because people are enthusiastic

As far as I know, no one advocating abolishment of software patents sees the need for an alternative. Fat32 is not in common use because people are enthusiastic about it, but because it's easy to implement, and it's compaitble. At a technical level, it's no different from trying to patent a database schema.