The difference is most likely due to configuration of innoDB, which takes a bit more tweaking than myISAM. The idea of innoDB is to keep most of your data in memory, and flushing/reading to disk only when you have a few spare cpu cycles.
You're saying right upto some extend. InnoDB is slower than MyISAM but in which cases? Everything is not made to meet everyone's requirements.
INNODB is a transactional database engine while MyISAM is not. Therefore to make it ACID compliance and transactions aware storage engine, we have to pay its cost in terms of response time.
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