He's not a good guy, but he never felt like the enemy either.
Exactly, he seemed perfectly reasonable until he went apeshit and tried to kill everyone. Individuals like that are by far the most dangerous opponents of all as you don't see it coming.
A Klingon will always be dangerous but everyone knows that they are, its the ones you don't see coming that you have to worry the most about.
Of course that is easy to say in hindsight, but Marcus made the mistake knowing full well what Khan was and he paid for it with his life.
Which is one of the biggest reasons I don't want Khan back in III. He's story is done, Marcus is dead, and he's back with his people--even if it is in suspended animation. Bringing him back, would cheapen his character.