I imagine it as following: Each gang as a paramilitary organization should be a subordinate of one of the major factions (Enclave, BoS, NCR, -some random fictional name-) out there.
It's not that simple to get it done and working, not at the scale you think.
There are certain problems with that, if these gangs under major factions are friendly and supposed to fight together under one flag, there are design flaws to what no solution exists. Imagine the possibilities of imbalance for a start, just think about it, that could be somehow regulated, but at the expense of free choice(only real way is to moderate population of certain faction, nothing is more effective than disallowing new members for a time period). If at some point imbalance occurs you might give better rewards for the faction with the disadvantage, but that is it. You can't disallow new members for the faction or something, its shitty concept to do that.
Now imagine enemy players using alts on your faction, looting stuff from faction members without permission upon fights and you can't kill him because if you do that there would be some kind of penalties of killing sub-faction members, right? So players would really take advantage of it and there is nothing you can do about it. There would be enemy friendly alts joining you to a fight to scout you and you can't get rid of him, if you do that many times logically you will be kicked out of major faction, Enclave, Brotherhood of Steel etc. etc. If that wouldn't be the case, these penalties for killing sub-ordinate faction members, then the whole system would lose the whole point of why such a system was made in the first place - to unite players, but it will do quite the opposite due to design flaws.
The biggest mistake what could happen is force the players upon such a system only, unique gangs outside of these factions is a must.
I'm just saying, don't hope for something like that.