In MyISAM, as a rule, there is little reason left. Later versions of MySQL (5.5+) expanded InnoDB to support all the features that were previously only available in MyISAM (for example, full-text and geospatial indexing), and InnoDB's performance is usually significantly better than MyISAM if configured correctly.
If you are not working with an older version of MySQL, or if you have every reason to do so, I would recommend using InnoDB only in any new database design.
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