Kill Ease
Underneath all that Reich brainwashing the Nazis are still men. They can be killed by any wound. Although the do experiment with eugenics and create some near invincible super soldiers (remember Hans from Wolfenstein 3D?), given enough bullets they will die. Zombies are a bit harder to kill. Only a head shot will do it. You can pump an endless amount of lead into a Zombie, but if there's no head shot they'll keep on coming. This can be bad if there's a large group of them and you're aim stinks.
Intelligence
Zombies are dumb - really dumb. They are unorganized, reveal their position, make a lot of noise and only have one thing on their mind: brains. They don't care about their own well being, nor do they know any better. They just keep on coming until they get you or you kill them. It makes for a relentlessly dangerous enemy. The Nazis are complete opposites. They are very organized. They tend to sneak up on you and can organize attacks. They are also harder to kill because they realize their own mortality so they hide behind things. While Nazis attack like a military body, they do have one bad thing going for them. They're loud. They yell and give up their position as soon as they see you.
Weapons
Nazis are the master of weapons. They will shoot back with everything you have and more. They always have the best and newest weapons. Nine times out of ten at one point in the game you're trying to steal their new super weapon. Until you get that BFG you have to fight through their endless machine gun and Panserfaust fire - not fun. Zombies only possess one weapon, their mouth. Although they can't kill you at long range, that weapon will make more Zombies. What began as one Zombie can easily become hundreds. The Nazis don't have the capacity to regenerate more Nazis. A single Zombie bite is fatal. Even though you could potentially live on for a bit, the bite will eventually be fatal, so any physical contact with a Zombie is potentially fatal.
Apperance
Zombies just look bad. They're clothes are all in taters and so aer their skin. Everything is completely decayed. The Nazis on the other hand have an elegant look of villany. Simple yet effective.
Mobility
Nazis have many means to get around. They run, walk, drive or ambush you in a tank. If there's trouble they'll be there fast and sometimes weilding nearly unstoppable weapons. Zomies on the other hand always walk the same slow menacing speed. Slow and steady wins the... brains?
The Winner
Nazis move faster, are intellegent and have the best weapons. Zomies look badder, are virtually unstoppable (except for destroying the brain) and have the ablitiy to create an army of Zombies. Nazis will kill you with a big bang and Zombies will kill you with one bite. Who's the better villian?
Sorry Zombie fans, but I say Nazis. These World War II villans are better than their undead counterparts because of their intellegence. While Zombies are physically repulsive and their attacks virulent, the Nazis equally match if not best the protagonist. They're basically you with better weapons. So why does the player always win? Simple - in the super effecient Nazi world the confusion of a single attacking outsider messes everything up. And that gives you the advantage.
