Excellent concept, except that Samus only removes her helmet after a mission has been completed. While on the job, she remains as fully suited as she can. When she can’t, you almost never know where she is. She was raised by the Chozo to be the perfect force for good, genetically modified to increase her body’s durability, trained in many different martial arts, and taught by the best minds the Chozo had to offer. Her armor reacts to all forms of damage, healing her and repairing itself whenever possible. The only upgrade Samus needs to defeat John is a missile upgrade, and she is easily capable of collecting more energy for her suit than John possibly can.
John, on the other hand, was also raised to be the perfect soldier, in much the same way Samus was. Unlike her, however, his muscular structure is almost entirely artificial, meaning it is unable to heal itself after massive exertion. This means that after a massive battle, John needs to be sent in for repairs, much like a Formula One car that has been on the track for too long. He has an advantage of a massive array of weapons to choose from, though he can only carry two at a time. His suit is not reactive armor, but it does carry an energy shield which is able to totally block a limited amount of energy weapons fire. He also has an effectively endless supply line to keep him stocked, and has backup at almost all times.
Take into account all these factors, and you have a really close battle. It would be almost impossible to determine who would win in a fight, unless Nintendo and Microsoft got together and made a pure Metroid vs Halo two player game. At that point, the winner would be determined by the better player. Anyway, why would those two fight? They’re both powerful forces for good, couldn’t they work together? (A co-op game with those two would be just as awesome as a vs game)
That’s about all I have to say, so, goodbye.