There was never a part in FO3 that I wished to be prone in.
Would it be nice to have maybe, especialy for a high strength sniper. But as most fire fights take place at close range. where the enemies rush at speed to close in range of you ( and add melee attacks as well ). And the lack of turning quickly would make it a poor subsitute for crouch.
Plus with the terrain ( maybe different in NV ) but in FO3 there were so many bumps, hills and other scenery and debris, that lying flat would not give a proper LoS.
The devs could have added areas where we could prone. Well they did. That crazy old sniper guy should have been prone. There are alot of time I wish I could be prone. Shooting while standing is hard but it is a game after all so I guess it does not have to take that into account.
Problems could be like you talked about is the ground. Clipping and falling through the ground could be problems maybe? I remember sometime ago said that enemies only show up within a specified area or frame, cell, if I am using the right terminology?. If we could prone that would give us a more stable way to shoot. Therefore we should be able to shoot alot further. With a powerful sniper rifle and great skills we should be able to shoot enemies miles away like in real life. Seeing as it's a game, not real life. The game can not handle this. So maybe not letting us prone solves this problem? would love to see enemies miles way. Find a nice spot on a hill side and pick people off from miles away.
Sorry if I am just talking crazy.. One reason why I like fallout tactics. I love picking people off from halfway across the level. Best sniper rifle, very high skills, and sharpshooter perk. Yes I mentioned Tactics again