There are 3 types of people posting in this thread.
1. People who have not read Halo novels, and thus have no idea what Spartans are canononically capable of doing and say MC would lose out of ignorance or based on what is shown in game.
2. People who have read the Halo novels and know that MC would be almost unsctahed by ME small arms fire and would run up to Shepard at 65mph dodging his aim (thus his bullets) with his 10ms reaction time only to grab his head and snap his neck.
3. People who have read the Halo novels and still believe Shepard would win. Those same people who are most likely typing from a padded room in a mental asylum.
Also, since we want to pull everything out of our asses to give our character the advantage...
Master Chief without Cortana Magic tanks atmosphereic re-entry. Master Chief with Cortana Magic tanks a gigaton nuke. What now?
Because we all know novel canon takes priority over game canon. Oh wait...
*Halo 4 spoilers* If the Didact wanted to, he could have killed Chief during that one scene. The only reason Didact didn't kill Chief is because of plot armor. (He is the main character and there are still two more games in this trilogy.)
Just to note: this is game Shepard and game MC. No novels.
Granted. It still comes down to the technology available to each, and Halo technology trumps ME tech. Precursors and Forerunners would sweep the floor with the Reapers, and Reapers are the most technologically advanced entities in ME.
So even allowing for Shep to have obtained reaper-tech guns (which, as far as I recall, he never does), the forerunner technology MC has access to beats it hands down. So MC has better physique and better weapons... why is this debate still going?