Another idea is that in Ep3 you take control of Chell and Gordon at different junctures of the game.
yeah, that's where i see it going - right now Gordon is somewhere in Europe whilst Chell is in the middle of a field in the US. It at least opens up a different location too. But yeah - i don't forsee HL3/Ep3 getting Gordon into the Portal world, meeting glados or -anything- like that. Hell, i don't even think Chell will have the portal gun if she makes it in - she'll be trading off the fact she's an 'abnormal specimin' who is too dangerous to test (as per the Ratman comic) and, possibly, psychotically diven. "Go and start a new disaster" "you want your freedom take it" - "that's what i'm counting on" still makes me think that GlaDos is using Chell for something - potentially something against what the Combine are doing outside. Or maybe the Gman is the person for whom Chell is "someone elses problem". I guess it's so stupidly open you could pretty much justify almost any jump -if- valve wanted to make it.
Also - in the shaft on the way out - you see a glimpse of something - 3 turrets and they are looking over something that looks alien. It looks like a strider... Or is it a massive overgrown potato?