Hey some nations you should add that have a real place in the fallout universe are The Jackels, The 80s, Yakuza, Iron Lines, Sorrows, The Texas BOS, a ghoul nation in Texas that hates and hunts human(From Fallout BOS) and The Hangdogs. You should also consider adding some tribal nations in the Midwest as lore states there are countless un-named yet powerful tribes out there. Then there is the Black Foot tribe, Twisted Hairs, Dead Horses, and some of the others assimilated into Cesar's Legion. It would be cool to have some of them at the start for 2 reasons A) You can build the legion into what it is in NV B) You can try to stand against the legion and change the course of history in Fallout in a major way, unite the tribes and fight back. Almost like Poland standing up to Germany
Now on to some home brew stuff. These factions I created to give my game depth in places Fallout is lacking lore and are inspired from lore and minor references thru out the varrious games. A tribe of intelligent death claws hiding out in the Louisiana swamps. These Death Claws are not non-violent but peaceful and follow a religion close to Buddhism as a way to control there bestial urges, they ware robes, build temples, and practice martial arts deep in the swamps. There called themselves the Yin Yang Zhǎo Nation.
Some Communist ghouls named Ejército Revolucionario De Decadencia ( Revolutionary Army of Decay ) R.A.D have taken over most of Cuba and are still fighting with The Outfit(
http://falloutfanon.wikia.com/wiki/The_Outfit ) the island is a war zone.
There are semi advanced groups of tribes that worshiped the founding fathers as gods that have spread there religion to much of North/South Carolina and the tip of Florida, they have techno shaman that use the gifts of the fathers(technology) to work miracles. Many tribes make up a unified culture and religious identity in the region, and all consider the coast from Florida to DC there holy land. Basicly a Tribal version of the BOS. There religion is called Founderism and they are refereed to as The Founders by outsiders.
In the Michigan area is ruled by fighting Biker nations who use the old steel and motor works to create there war hogs and ride out on raids against each other and tribal groups in the area (Picture vikings with Motor Bikes instead of boats) sometimes they have united to fight people like the East BOS. The names of the various gangs range from Midnight Riders to Motor Angels, but to outsiders are known as the Steel Horse Raiders.
The last faction I added to my RP game was in PA where a group of Neo Amish/Neo Anabaptists ruled and were completely none violent against anything human, however they didnt consider ghouls or cannibals human anymore( Think East Coast New Canaan equivalent). There territory was central PA and up into NY state a bit. They call themselves the United Anabaptist Church.
There were plenty more but these were the big ones that the party seemed to enjoy the most.
Fun side note in my game Mexico had 100,000s of Mister Handy's everywhere cause in the Fallout lore a huge earth quake hit Mexico city before the war and tons were donated or bought by the Mexican government to help with clean up and reconstruction. Not sure how you could fit that is but it was one of my parties favorite parts.