Hi
I have been researching the differences (implementation as well as performance) between MyISAM and InnoDB for sometime. It looks like we need to hit a subtle balance between both of them,
In particular, it was very disappointing for me to read that Dani had to revert back from InnoDB.
The right way to use the mix, IMO, is to use a master-slave configuration for database replication. One should use InnoDB on the master to store tables for fast concurrent inserts and updates. The same table should be replicated on the slave using MyISAM for fast reads.
Also, when using InnoDB, don't forget to play around with the innodb_buffer_pool and innodb_thread_concurrency parameters. They seriously impact the performance you get out of InnoDB setup.
One last point to note here is that InnoBase has been acquired by Oracle already. So, future bug fixes and improvements may not be free.
Hope this helps!!