For the purposes of this battle, assume that the ME and Warhammer Galaxies are relatively close together.
Hey, man, say that to Microsoft and/or the videogame producers and publishers related to the Warhammer series.
Of course Mass Effect would lose. The Reapers are the toughest thing the Mass Effect universe has to offer so far. Edit: Though the Reapers would offer the strongest fight out of all the factions in Mass Effect.
The Reapers seem a lot like the Necrons to me. Personally, I reckon the Mass Effect humans would be easily converted to the Imperium; true, they consort with disgusting xenos, but the Salarians should convince them of humanity's superiority. And if not, at least Shepard seems like he would make a decent Rogue Trader.
Get rid of the genophage on the Krogan, have a cultural renaissance and BAM! instant horde of Krogan.
They're called bolters and the Imperium use them. And SOMEONE here is just lazy and overly incompetent, incapible of coming up with even the least meaningful of rebuttles. Instead, they attack canon sources and claim that they are not canon, for which they have no proof whatsoever and the proof of the matter is in fact in the opposite direction, which they blatently refuse to acknowledge, no matter which way the argument is going.