I feel like being a killjoy and trying something legit. Gordon, in the wake of Elis death, goes and tries to destroy the Boriales with Alyx. The G-Man attempts to intervene, but is blocked by the Vorts. In there travels, they are briefly helped by a confused young girl with a gun that shoots Portals. After running a gauntlet of Combine forces, includeing a rather whimsical AI that had been cut off from its combine roots, they learn that the G-Man was originally hired by the Combine to smooth over the takeover of worlds from other dimentions. They destroy the Borealis, foiling the G Man, only to immediately realize that the G Man was a turncoat who took a bunch of alien technology, and started pursueing his own agenda of secureing earth against the combine. He even had earths military in control of Xen briefly, but the combine overtook them easilly. He realized he had to act through agents, so he set up Gordon to be this charismatic messiah figure in opposition to Breen, the G Mans replacement. The Borealis was his trump card, a trap right under the Combines noses. Never one without a contingency plan, the G man plays all of his cards, digs out Adrian Shepard from stasis, and uses the humans portal technology to launch an unexpected assault on the Combines headquarters in Xen, while Gordon goes in the proverbial back way to take them down from the inside. Finally have a big advisor fight that Gordon wins that cripples the Combine beyond repair. I think that story would be fairly well supported from information you get from the games, and is a fair guess. Of course, they can't end it on a total happily ever after sentiment...Something will happen that shows that theres still stuff to do. No clue what it might be.
I don't think Valve would be so Cliche as to kill Gordon off, but I bet he will have to make some sort of sacrifice. He has just been shown ass too Messanic to not have some big sacrifice. But in the end, he has to get the girl. To throw out something completely Fanfic-like, unsupported by evidence, maybe him and Alyx get trapped on Xen after saving the world, with the last Vestiges of the Combine and the naturally beligerent Flora and Fauna. Wraps up the arc quite nicely with a sense of completeness, but still leaves room for a sequel with new intrigue.
The going back to half life 1 idea isn't neccisarily all that bad, if you twisted it a bit. Say, if episode 3 wrapped up with a nice ending, and the only way to make sure it was nice is if Gordon traveled back in time to the very beginning of Half Life 1, and played out events in the exact, intricate manner that they occured. He would be so quiet because he doesn't want to alter the time stream, and he is obviously a badass with weapons even though hes a scientist because he has all that practice. Or something similar. Wakeing up from a dream though...little too weird for my taste.