The only reasons to use MyISAM in versions of MySQL prior to 5.5, was that InnoDB did not support partition tables or create FULLTEXT indexes.
Those restrictions no longer exist.
The only reason to use MyISAM is that it is faster to read and slightly faster to insert (in mass and measuring an isolated process), but that is because such operations effect a table lock.
If you are going to have multiple updates, or concurrent entries, for example, a table-level block is very inefficient , versus an update on an InnoDB table that uses blocking at the level of row , and therefore allows concurrent operations.
Add to all that InnoDB allows the use of foreign keys that are indispensable to maintain the referential integrity of a data model, the support for transactions.
In summary, use InnoDB because
- In the current MySQL version it supports everything that MyISAM supports
- Foreign Keys / Relational Integrity
- Block level blocking
All these advantages far outweigh a decrease in speed of the select.