Mordekaiser is extraordinarily squishy in his early game, for a bruiser. And he is paying out health much faster than he can regenerate it, as well, just for using his abilities. Harass him in the early game, and he will have a bad late game as he fails to get his farm.
Also, Morde gets 35% of his damage (NOT reduced for AoE abilities, like Spellvamp is) to his shield. THAT is why he is so tanky in the late game. The more magic resistance you have, the squishier his end game gets. I'm not even kidding, countering his damage output counters his defenses, too.
Mordekaiser is actually considered underpowered these days, as I recall. A little bit of planning and preparation, combined with knowledge of his abilities, makes him fairly easy to deal with.