We are using myisam primarily for full text on mysql 5.5 ,However as 5.6+ innodb supports full text i want to know any performance or other bottleneck ,Please suggest ,we have huge data set in millions and currently tables are mix of myisam and innodb.
Oracle's goal seems to be to get rid of MyISAM. Version 5.7 has virtually all the improvements to eliminate the 'desire' to use MyISAM. The next version, 8.0, is attempting to finish the task -- including getting rid of the MyISAM tables from the
mysql database. (cf "Data Dictionary").
The only thing that remains is disk space. Any InnoDB table will continue to take 2x-3x the disk space of a comparable MyISAM table. But disk space is cheap and SSDs are prevalent, so this is not a big deal.
I strongly encourage to make the shift. See my article for some rare gotchas that might bite you in the conversion. (Which reminds; I should update it to say more about the status of 8.0.)