The remnants of the Master's Army, really shouldn't be popping up near Boneyard. I know the Cathedral was there but it was mostly full of humans, and in the lower sections only a few big guys. Also it makes it near impossible to get through there and get any XP, you ever try going up against a rocket launcher to get kills on molerats and dogs. Guess who's gonna kill them.
San Fran, EXTREMELY difficult to travel around!!! A friend and I were doing the train quest we're both 4th lvl, and he had 75% outdoorsman and we were getting encounters every 2 [tiny] dots. And the first was centaurs floaters and tough aliens, we managed to just barely get out, next was Mercs, who managed to 2 hit us from ACROSS the screen, well out of our attack range with their one Energy Pistol. From then on we respawned near San Fran, and hit EVERY encounter not a single one with the option to avoid. And until we passed Vault 13 it was ALL Centaur, Floater, Aliens. 2 more deaths later respawning [you guessed it] San Fran, we made it to NCR. I know the need for higher powered encounters but I really don't think they should be in the MAIN path between towns.
There is NO chance for low level people to get anywhere with how slow the travel is, and with even 75% OD, being stuck in encounters more than 5 times in a square. We couldn't even get the option to avoid RATS...