hints towards GLaDOS being a feminine and inorganic parallel to the Breen Slug from Epistle 3.
I could imagine hidden backstory for Aperture like stumbling upon Xen teleportation experiments and the Combine having an alliance with Aperture Science. I think EP3 would be some inter-mixing of Half-Life and Portal's worlds and elements, a lot of mind boggling and eerie parts of Aperture that would seem like some kind of insanity inducing reality defying maze of madness, though Portal 2's tone is way too campy for Half-Life's existentialism and Lovecraft themes, if done correctly, it could be something really interesting.
That EP3 map pack was definitely a nice attempt to see what an actual EP3 would have been like, though taking in context of Epistle 3's plot, it's much too short and has no surprise twists or plot developments other than find Borealis and destroy it.