Sure, for a transactional database InnoDB is a slam dunk. MyISAM doesn't support transactions or row-level locking.
But what if I want to do big nasty batch queries that touch hundreds of millions of rows?
Are there areas where MyISAM has relative advantage over InnoDB??
eg, one (minor) one that I know of ... "select count(*) from my_table;" MyISAM knows the answer to this instantly whereas InnoDB may take a minute or more to make up its mind.
--- Dave