Re: Different ibdata files for every database

[Marcus Bointon]

There is a way you can achieve this: run multiple instances of mysqld on the same server. This is often done by those wanting run run a single machine as a slave to more than one master.
The other trick is to make sure you use innodb_file_per_table as that leads to more efficient use of disk space. As far as I'm aware there is no way to recover space used by ibdata files other than by starting again with a clean install and reimporting data. Personally I think that's a big enough problem that it should be regarded as a bug.