My plan was always Campaign play. I have been a little pressed for time as I have been running a D&D 3.5 sandbox for the last year, so I admit I have not done more than a passing read of the core Alien book. My first idea is to use Delta Green adventures and adapt them. I will probably have the players be in the vein of space truckers with room for corporate spies to be crew members, or retired colonial marines. That way all the careers are essentially available.
A suggestion I have is to make your own evil Corporation. The novels often reference rival smaller corps. This will give you the GM agency to do things with the corp that you couldn't do with WY including having your party actually defeat them.
I don't plan to whip out the Xeno's themselves until much later in the campaign. There are plenty of other critters to wrestle with as well as androids and space pirates etc. I plan to leave bread crumbs along the way about the Xenos. The conceit about this game is that its called Alien, we all know they should be coming at some point. The key will be to make it matter when they are introduced.
The 'mcguffin' campaign idea is pretty easily used here (though I lean on the trope too often). The party has something, most likely information about the xenos or maybe even someone in cold storage who has been impregnated, and corps will literally kill to get it.