With MyISAM tables you could have integrity problems. And if you are mixing innodb and myisam you are splitting buffers memory that well could go to just one kind (i.e. most memory for innodb) if you switch to that. If innodb is slow in insertions, you could try using TokuDB as storage engine, that is pretty fast in that and have a bunch of advantages. And if you are using MyISAM for some particular feature (i.e. full text indexing) MySQL 5.6 already have it in innodb, or you can separate that search to a sphyinx server.