They already went an alien direction in Fo3, so they wouldn't want to repeat that again in another add-on (even if it's not in a space ship).
Now if you're talking about Area 51 just being a place with advanced military technology and a bunch of secrets, well Old World Blues (or whatever Add-on that will have The Big Empty in it, but I think it's OWB) is going to have The Big Empty which is a "Treasure trove of pre-war technology". IMO The Big Empty sounds much more interesting then some military base. Besides... does anyone else think that the whole "Area 51" thing is a bit cliche?