Personally, I would like to see more random encounters with already established characters sets. Say, perhaps with the mutant army remnants hiding out in a cave (like the bandit gangs) or maybe a BOS patrol. Also, in the SF area, the interesting thing is that the Hubologists seem to control the entire SF basin, along with press gangs, death claws, and mercenaries. The Shi, who run SF, don't even has so much as a gate guard. Given the fractious relationships there (especially with the press gangs and mercs) how could the Shi not have any defenses or ongoing patrols? That just doesn't seem to make any sort of tactical sense to me at all. If that were the case, they would have been overrun decades earlier.
Oh, and BTW, as for using the BOS facilities as weapons and ammo storage, one really doesn't need them for that. In SF, Dr Fong's anteroom, the two lockers in the front room seem to be limitless storage. Also, you can easily use Lara's place (even before taking out Tyler) and she doesn't seem to mind; in NCR, you can use the Captain's gate house (in front of the gate) if you first kill her with 9 Super Stim Withdrawal. It doesn't seem to affect your karma either. Just be sure that you first enter NCR at least once so that you can re-enter the city from the world map if the laser force field is up. Otherwise, there would be no Captain to lower the force shield gate for you.
Insofar as NCR is concerned, I'm still a bit put off by the lack of other people and houses there. Yes, I do understand that there is a finite number of things that can fit onto one screen, but there should at least be a few basements, and maybe an attic or two. I mean, even Modoc and Redding has underground tunnels. It's like people in NCR forgot how to build structures (except for the bar basement). That is, I would like to see a bit more fleshed out expansion in the NCR set, even if there isn't any more quest material.
And how about finding random basements in the random maps of destroyed city streets? The nature of the game content doesn't change, but the level of randomness and encounters can be dramatically increased. I think players all want encounters of some kind in these games, so by putting in more nooks and crannies, it would fill a hunger but do so without altering the game much.
I still find it oddly unfair that killing Japanese mobsters begets karma gains, but killing American mobsters loses karma. The same goes with killing the guards on the "bad" caravans. The evil caravan boss will result in karma gain, but killing their escort is apparently a bad thing.