Portal 2's Co Op, assuming it's Canon, has notable effects on any potential Half Life 3.
You launch War Drones. It's played as a one off joke, but, her facility is allegedly ~1 Massachusetts Large. And she repaired it back to almost new in a couple hours.
Invading Aperture is a thing you can not pull off.
"But Aperture has no real reason to care about the Combine though!" I can hear you asking, but actually, she does. The people she gains at the end of the CoOp are pretty much all dead within a week, if I recall my lore correctly, and she released Chell. And clearly Atlas and P-Body aren't quite cutting it any more.
She's going to start making noise (The drones we released during CoOp), attracting the Combine to her relatively small above ground facilities. They're going to try to enter. And they will.
The first time, they'll be met by Atlas & P-Body and some turrets, and stripped of their technology for Glados to Study.
After that, for the most part, Combine entering the building will be high speed Emancipation Grilled, and sent for testing. Glados of course puts up the persona of this being a resistance base, a big one, aggravating the Combine all the time so they send more soldiers.
At some point she reveals the portal gun, and the combine of course freak out - Lets be real, it's miles ahead of what they or Black Mesa ever developed.
They call in reinforcements from other dimensions, and Glados, being a smart cookie, takes advantage, capturing yet more alien tech, learning from it, and reverse engineers her way to Xen.
And at that point it's all over. She can grab anybody, from any universe, for testing.
Heard of the Portal 2 Perpetual Testing Initiative?
The Lore?
She has contact with parallel Apertures, but more importantly, parallel universes full of test subjects.
I submit that the players in this mode are in fact Combine, at least at first. Until they're all dead.