Do i have to bring up the reasons why snake can beat *insert name here* again?
Ok, face it. Sam has never fought any SUPER SOLDIERS nor giant robots capable of leveling an entire city.
Sam is also "weaker" than Snake. Getting shot with an assault rifle will not stop Snake, but it will stop Sam.
CQC > Sam.
If sam tries to stalk Snake from above, well, snake can just put on his thermal vision and GG hes dead.
If Snake tries to stalk sam with a box, GG, there are no equipment sam has that can see through a box i believe.
Also, age factor seem to not affect Snake because in MGS4, he appears old.
Thus, add all the equations together, we get... snake >>>>>> sam.
