I never thought that BOS in Fallout 1 made no sense. It's nice to bring the things through that angle. Insteresting also considering that BOS were made as a counter-part of the Guardians, an hostile faction in Wasteland 1.
I would also add that it seems that the increased role on the BOS in the Fallout franchise seems not much related to Black Isles, the Original develloppers.
During Fallout 1, The Unity and the Brotherhood of Steel were like the two most important faction.
It is particularly true with the Unity, while the BOS are mainly the strongest faction that provide help agains't them. (one shouldn't forget the role of the Followers of The Apocalypse and the children of the Cathedral, both involved in the main plot)
By the time we got to Fallout 2, still by the original develloppers, the BOS and the Unity are barelly there.
You meet three guys from BOS wearing only metal Armors. Personnally, i played Fo2 before Fo1, and didn't suspected they were importants in other episodes, by judging these three guys only.
The Only unity members are in random encounters. Broken Hills super-mutant are no longer part of any unity army, while Mariposa super-mutants has no connections with the Master.
So, by the time the Chosen One start his quest, those two factions are minors at best, quite none existant at worse.
If Black Isles remained the only develloppers, we could assume that those faction would have totally disapeared before Fallout 3.
(with maybe some ex-member met from times to times)
Then we have interplay...
I don't know if when Fallout Tactics and Fallout Brotherhood of Steel were released, the CEO was still Fargo or already Caen, but the fact is that those games were initiated by the publisher and not made by the original devellopper.
Those two games aren't RPG, are more combat oriented and target a different audience.
Both games intend to make your characters be part of an ongoing war, based on Fallout setting.
As the war already started, it allowed the player to be lauchned in the action at the beginning.
So they choose to pick already existing factions, for the most part.
They choose the BOS as the main good guys, as your own army, simply because it allowed you to have access to all gear available, from the worse to the better, thanks to you quartermaster.
The major ennemy was the Unity, as they are more recognizables, popular and impressive. Plus, if they had chosen the Enclave, your ennemy would have looked too close than your allies.
But those two games hadn't high res graphics, and you could choose to drop the turn-based, and get a fast-paced gameplay. In fast paced gameplay, you better recognize quickly your ennemies, as they're creatures/machines.
So we got two games that provide a larger role to the BOS-Unity war, than they ever had in Fo1.
But, even if they choose to turn Fallout world into a battlefield, they used a way that remained consistent with Black Isles already done world. (and even chose those devellopers to do the third episode, the Van Buren one)
In the Timeline, Fallout Tactics and Fallout Brotherhood of Steel are supposed to take place BEFORE Fallout 2.
So, even if during those two games, the BOS and the Unity are two of the largest army of the Wasteland, it still doesn't prevent their downfall by the time Fallout 2 happens.
During that timeframe, the cohesive army that managed to survive the loss of the Master, the Cathedral, the Lieutenant, the Vats, Mariposa, was still able to fight back and lead research under the leadership of Gammorin/Latham/Attis, before being crushed for good by the BOS.
The BOS itself spent many ressources on these wars agains't the Unity, the Calculator and the raiders, and splitted when they lost communications with Midwest chapter. They were pretty weakened, by all these wars.
So, even if they are overpowered in FoT/FoBOS, the unity & BOS could still be the shadows of themselves by Fo2, and probably long time dead by Fo3 (Van Buren)
Then, Bethesda bought the licence and wrote their own Fo3, only by reading the summary of the previous episodes.
They seen that Unity and BOS were major factions in three games out of the four availables, so they didn't hesitate to include BOS and super-mutants in Fo3.
As Fo3 is action oriented, they also given the protagonist access to their gear.
As it is even more action oriented, they provided various kind of power-armor, allowing the Enclave to come back, as they have even better stuff than BOS and created the Outcast for those who want a red power-armor.
Except that they don't even care to make it happen before Fo2, even if it would be more logical than 200 years after the war, considering that everything looks like the bombs fell yesterday.
Now, we have New Vegas as the last episode from the series and from the original develloppers, Black Isles/Obsidians.
As we could notice, The Brotherhood of Steel, the Unity and even the Enclave are still the shadow of their former selves, as it was probably intented if they had remained the sole develloppers of the series.
So, they leave room for other factions to take the torch.
(i would even say that they could have even removed them if left the choice)
We could assume that if Obsidians make a new Fallout, House would be dead, and the NCR/Legion would have lost most of their power.
On the other hand, if some publisher/devellopper still want to make some spin-off like FoBOS or FOT, they could still use the BOS, the Legion , the NCR or Navarro personnal, provided these events would happen BEFORE Fallout:New Vegas.