The MySQL optimizer makes the decision of what execution plan to use based on the information provided by the storage engines. That information is not accurate in some engines like InnoDB and they are based in statistics calculations therefore sometimes some tune is needed. In InnoDB these statistics are calculated automatically, check the following blog [...]
InnoDB Full-text Search in MySQL 5.6 (part 1)
I’ve never been a very big fan of MyISAM; I would argue that in most situations, any possible advantages to using MyISAM are far outweighed by the potential disadvantages and the strengths of InnoDB. However, up until MySQL 5.6, MyISAM was the only storage engine with support for full-text search (FTS). And I’ve encountered many [...]

