My, my, my, it's been such a long time since I've seen a thread that truly caught my eye like this one! Reading all of your interesting theories, I figured I might present my own.
To begin with, when you say "Shapers", which group do you mean? The loyalists or the rebels? And, even then, you've got the human rebels and the creation rebels.
Anyhow!
The Empire vs. The Pact:
The Empire. Don't get me wrong, I think there would be a good fight, but I also think the Empire would completely overwhelm the pact. There's just too many of them. The only chance the pact would have, I think, would be getting a portal pylon (I believe that's what they're called in the Avadon games, it's been a bit since I've played them) literally directly inside of the current leader of the Empire. It seems too implausible. Not impossible maybe, but very, very implausible.
The Pact vs. the Shapers:
This depends on which side you're looking at it from. Are the Shapers attacking the pact, or is it the other way around? Maybe the rebels trying to make a foothold on new land?
If the Pact up and out of nowhere decided to attack the Shapers, they would be decimated. Destroyed. Blasted and burned and melted and electrocuted. The Shapers would most likely start out with that maritime nation all the way to the west that I can't remember the name of and spread their forces from there, gradually either assimilating the remains of the Pact or destroying it.
On the other hand, if the Shapers decided to attack the Pact, they may have a chance to retaliate. The Pact has, quite possibly, the most knowledge of portal and transportation magic. If they could transport assassins into a few major Shaper strongholds, the Shapers would be left leaderless and confused.
Rebels are a different story, though. In the case of the Rebels vs. the Pact, I have a feeling that the nations of the Pact would, quite literally, be razed to the ground, regardless of who attacked who first. The drakons would unleash maybe a score of Unbound, spread across the continent, and, barring any miracles, the Unbound would do their work astonishingly well.
And so it comes to the Empire vs. the Shapers. Personally, I don't know if the numbers would matter so much in this one: it IS true that the Empire has significantly more warriors at their disposal, but at the same time there are several hundreds, if not thousands or tens of thousands, of Shapers: and each Shaper is an army. What it would come to, I think, is who has a better understanding of magic. The Empire would win, I think, just because they have basic understanding of teleportation magic: which, though it exists in Geneforge, is so unpredictable and difficult that the Shapers have more or less given up on it. The Shapers are better at Shaping. That's it, though. They're more or less one trick ponies. And that, I think, would be their downfall.