I am not a database engineer but I do know that innodb is sometimes faster than myisam. Here is why...

MyIsam will not allow any transactions while another transactions are taking place. This is useful for things where you do not want things to be overwritten or performed at the same time, such as incrementing values.

InnoDB will allow other transactions to occur simultaneously.

Each storage engine is meant for different things, but normally, people will choose InnoDB because it wont block transactions while others are taking place.

More information: http://stackoverflow.com/questions/12614541/whats-the-difference-between-myisam-and-innodb