Easy solution: Don't make a level 6/6/3 mind-flayer fighter/rogue/assassin just make a level 15 mindflayer assassin.
The problem is how much guidance the game gives you to make a mind-flayer who has some sneaky attacks, and can also wield a mean longsword on the frontlines.
The 4e approach is to tell you what the defenses, attacks, and hp should be for a creature of that level. Level up (or down) your mindlfayer to the desired level. Then look at some NPC rogues, assassins, and fighters. Take a power from each and add them to the mindflayer. He should be as powerful as two standard creatures of that level.
3e didn't give you that guidance. Instead, you added class levels. So if you wanted him to have a power that a sixth level fighter could have, the sneak attack of a sixth level rogue, and the ability to cast a spell like a 3rd level assassin, you were suggested to go ahead and add all those class levels, which gave the creature more than you needed, and likly put the creature beyond the range of your players' ability to fight. Or you could wing it. But if you were an inexperienced DM, that was a scary prospect and for good reason. Winging it was not easy. Your mind-flayer might end up being overpowered or underpowered. You had not rules of thumb to gauge whether you did it right. (Heck, the CR system in 3e was so borked even when you did it by the book, you didn't have much chance of getting it right.)
As far as I'm concerned, adding class levels is appropriate if the class has very static bonuses (like AD&D fighters). Otherwise, it's an exercise only for the DMs who are not particularly concerned about balance, or for recurring villains who need to be fully statted.
For everyone else, the game needs to have guidance as to expected defenses, hp, attack, and damage for a monster of a given level, and guidance on how to add a few powers to a creature.