I think whatever ability the mind flayer gets, it should make for a good boss. Right now, the mind flayer has the same problem a beholder has: it's all offense. But if you're a boss, you gotta have some staying power. They're not very scary if one beater can just charge up and go "THWACK! 48 points of damage! That's that!"
How about the flayer being able to set up some kind of deterrent effect around himself? Maybe a charm monster or confusion aura, or a simple repulsion effect that keeps opponents away? Is there any psionic power that would effect this?