There were actually some "facilities" at the beggining of the game, but like in almost every single videogame out there, the level of detail from the first part of a game is usually better than afterwards.
There are 2 main reasons why that happens:
-There's less need to catch the players attention to play the game, so you can reduce detail while making combat more present. (you already beleive you are in that world, it's just a matter of shooting bad guys now!)
-The other reason is that at the beggining of a project, the team is usually much more motivated than in later stages, when concept art becomes less important and debugging is the main worry... : Like Michael Abrash (ID software) once said:
"When you are done with 90% of the game, you find that you need to work on the other 90%"Back to the topic: if we consider that Nihilant was under the Combine's control (like Breen was), it's quite possible that the combine had already captured a large number of xen individuals, including headcrabs, vortigaunts and even a bigmomma. It would explain why Xen sometimes looked a bit deserted, in decadence. They probably experimented with headcrabs and that's why we see other species in HL2...