Clearification time children!!!
Race-X is a collection of species from a different world, in fact, different dimension than Xen.
Adrian Shepherd was not placed in stasis by the G-Man, he was transported to a a place occupied by an ungodly large army of Xen/Race-X creatures. Meaning, he was sent to die.
Alyx is wearing a Black Mesa sweater because either A: she got it from her father. or B: she was given one when she visited there with her father as a child.
Well, those or she just thinks it looks cool, who knows.
The headcrabs are back in the sequels because many were already here on Earth when the Combine arrived. Many mutated over time as they possessed people and were also genetically altered by the Combine as they experimented on them to use them as psuedo-biological weapons. Valve said the poison headcrab was actually intended to be in the first game, but were left out.
The combine have not conquered Xen, as they have been unable to reach it. One of many reasons the Nihilanth race fled there to escape the Combine. This is also why the Combine were so interested in Kleiners teleport technology as it used Xen as a sort of waypoint to teleport matter from place to place on earth.
And now, speculation time!
I'm not sure they'll be an end "boss", but full grown advisors, as opposed to the larval ones in Ep1 and 2, are a very likely enemy in Ep3.
I'd love to finally hear Gordon say something, but I just don't see it happening....ever. (he is mute after all)
Regardless of whether there's a boss or not, I think there could be a moment where Gordon has to sacrifice himself to save the world, or in the very least Alyx. Thus cementing his "christ-like" image to the people in the story. Or they may have Alyx sacrifice herself to save Gordon, who knows.
Breen is another possibility, but I firmly believe him to be dead.
The return of a Nihilanth would be an interesting twist, but an even more interesting would be allying with one to defeat the combine as they are our mutual enemy.
What ever the outcome, I can't wait. Sad there won't be a Half-Life 3. There may be other Half-life themed games, but none with the one Free Man.