Have you really used performance metrics using the myisam and innodb tables? In my experience, the speed difference is not really that big when you consider all the ACID benefits you get from innodb. Only locking a table in itself will affect speed, so innodb will be faster.
Also note that myisam is much faster on inserts, not on choices. You insert only 5% of the time ... do the math.
You can always use mysqldump with innodb, so your backup process is the same.
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