The character interactions. Picture Solid Snake meeting Naruto. They come from such different worlds, but they both have a sense of justice. Their conversations and how they learn from each other can be really engaging. Maybe Snake teaches Naruto about more practical ways of combat in a modern - ish world, and Naruto shows Snake the power of friendship and believing in oneself.
The combination of different abilities. Naruto characters have ninjutsu and chakra powers, while Metal Gear has advanced technology and stealth skills. When these are combined, like Naruto using his Rasengan while sneaking around Metal Gear's high - tech bases, it's really exciting.