Shepard and his army. The UNSC soldiers are useless because they can't shoot or drive, and the Covenant soldiers consist of stupid gorillas and little purple cowards called grunts that shoot green goo.

master chief could beat all of shepards army and his own if need be by his self. 
 
 
by the way even chuck norris is afraid of Master Chief.

Wrex.  No question.

Fiction-wise, obviously Master Chief.

Idk.  It's kind of unfair when one side has the fucking force, but MC with Spartans, Elites and Hunters would fuck some wannabe Jedi dudes up.  

Couldn't the biotics just instantly immobilize the enemy troops?
 
Seems like a no-brainer for Shepard.

Shepard would use his wits and charm to get Master Chief to have sex with him.

Master chief survived a fall from fucking space, Shepard didn't. END OF STORY!!!

Shepherd has singularity.

I'd probably lean towards halo because of master chief and the elites.  I don't know though, it's kind of a stupid question.

Master chief is a super soldier, Shepard is a regular guy.

When shepherd fell from space onto a planet, he died. He came back, but not because he's badass.
The chief survived that scenario not one but two times. Because he's badass.
 
Not to mention Shepherd never really has to deal with vehicles of any sort and pretty much just fights primitives and robots.
I think a chief on Shepherd fight would go hard in the Chiefs favor.
 
However, the UNSC isn't nearly as large as the council, geth, and and alliance navy's. We're talking billions of people and billions more robots.
All the UNSC has is whats left over from gaylo 3 which isn't a lot I'm guessing. And the Elites pretty much got smoked in Halo 2. 
So that wouldn't go very well.

" Shepard would use his wits and charm to get Master Chief to have sex with him. "

Super Meat Boy.

" Super Meat Boy. "

Based on the fiction the odds are stacked heavily in Master Chief's favour. 

Shepard, easily. He has Biotic powers, and his whole team would have Biotic powers.