They're both cartoony, they both have classes, and they both are more fun with teamwork. That's it.
Having played both, MNC is completely different compared to TF2. MNC is more like DOTA crossed with a third person shooter.
Hell, MNC's Assassin isn't as brutal as TF2's Spy. Assassin's equivalent to the backstab can't oneshot a Tank or a Gunner (Think TF2 defensive/offensive Heavy) consistently.
She's unbelievably hot, though. Even if you can't see her face.