Populating cities theme vs. visible bases:
There is opinion that empty cities are here because of PvP in cities :/. But ok, i understanf what you are afraid of and i am offering little solutions:
make a general reason why to visit cities and individual for each city:
1) to upgrade your bases, you need parts that could be founded in city NPC. maybe you could add purpose to speech skill. with enough skill, you will be able to talk with no-talk npc and trade too.
2) to maintain your bases as i suggested, you need water, so in HUB city, you could buy water caravan and with your teamates you will have to carry it safely to your base: another reason to visit HUB + enabling team PvE
3) you will need special el. parts or something electronic, you will only find in Necropolis vault => another PvE element, reason to take anti rad drugs, or this can highly boost scavenge roleplay and player interaction.. you could trade this parts with non pvp players.. and where? in cities
4) if you erase stupid chemical components and you will bring back drugs from meat, meat from brahmins, you could enable brahmin markets and players will go more often to cities to buy brahmins for a meat
5) special bonuses for your visible base if is placed near specific city:
HUB: quest that you will get some water to your water tank for free
Gecko: same but instead of water -> el. power
Klamath: free brahmins => more meat to drugs
San Fran: instant medical station upgrade
Junktown: free dogs = dog will detect sneaker
i think we would find more ideas, if we try
Because of this, you will spread bases across the world map. base members will first check their nearest city for stuff. and maybe players will buy a car to fast traveling..
6) maintain element in your base, upgrades, .. will push you from the base, instead of lock you there
7) imagine player RP traders in visible but safe bases => they could open their markets near worst pk city and they could be still in safe
i wrote it before: base with newbie barracks will help us attract and hold new players. we had cca 20-30 new members, but only few of them stay with us because of reasons i described before.
9)people need chalenges - this will hold them in game and cities will not be so empty
10)also there could be pve .. defend your base from time to time, more fun, more people, more life in cities
11) every era, you implement new economy changes, that did not solve anything important, focus now on base economy instead of player economy
So why not?
P.S.: i was afraid to visit cities because of militia