One on one Brettonia would win but the empire has a lot of allies and so does Brettonia... -SNIP-
That doesn't correlate to the OP's question. The idea was to disinclude any and all outside forces. Besides, even if other factions were to be included on any and all levels, the Empire would still hold out longer than the Brettonians would. I doubt the Bretts would ever be able to withstand a Kislev-scaled assault like the Empire did. Nor are the Dwarven or High Elven empires comfortable in working with a faction that is just as, if not moreso, isolationist than even themselves.
On a strictly one against one basis, the Empire would win for a long variety of reasons. The first, and I hesitate the draw parallels between such a fictional world and our own, is the Empire's judicious use of gun powder. Historically speaking, we've seen how powerful a musket line is against any form of armor, even, in this case, Brettonian armor. The shear capacity for the Empire to field it's array of war machines of Nuln or any other providence alone is enough to do in the bulkhead of the Brettonian army - it's heavy cavalry.
Another factor, and one that has been mentioned already in this discussion, is the principle of relative population of the two factions. The Empire is far larger and more populated (in terms of military service-quality people). It can field a larger force far more rapidly than the Brettonians. It is much cheaper and easier to field a large unit of foot soldiers, such as halberdiers or spear men, than it is to field even a small unit of knights. All that it takes to go into putting a spear man to the field is a long stick with a pointy piece of metal and a slab of wood, maybe some nice-looking clothing. For a Knight, it takes a full suit of armor to be either handed down or custom forged, a lance, a steed of high quality and is well broken (it's an equestrian term, Google it), and any other Chivalrous accouterments that said knight would prefer to sport. Those two examples, mind you, represent a linchpin unit for each faction. It clearly makes sense that the Empire's infantry are easier to field (despite being fairly well trained) than the Brettonian knights (who are, individually, the greater warriors).
I could go on, but my point is clear at this point. Isolating the focus of the debate solely down to the forces to be mustered, the Empire would win. In game terms, I cannot say. But with history as a precedent and logic and a basis, we should be able to judge the Empire as the preferred victor.
I would also imagine tactics are more than worth noting, but those are so subjective that it's folly to bother including in a sensible argument. Who's to say that the Empire wouldn't love to see the heavy cavalry of the Bretts charge up a steep slope (a la Agincourt)? And who's to say that the Bretts wouldn't like a large, open, flat field to allow their great cavalry the opportunity to out-maneuver the vast hordes of the Empire (barring any intervention of the Knightly Orders)? This is all very, very subjective and it's easy to get ourselves caught in a cyclical debate of "Yeah, but if..." We'd clearly have to look elsewhere to establish a more respectable, though hardly definitive, answer to the OP's query. Hence why I mentioned the forces only.