The citadel would have been a more darker place, with more horror in it as well, the idea of the Citadel being alive was there for some time, playing in this place would be just really boring and disturbing, it's a great design of course but, it was just really dark
some character concept would have been just really hard to adapt into the 2001-2003 source engine, the first one (a beta Stalker npc) already was finished
i feel like, if valve stuck with the beta storyline and all the other things from it for hl2, it would've pass like just another 2000's horror game, same as "you are empty"