There is one place the Enclave could have a hidden base... in orbit. In FO3 Broken Steel the Enclave had access to orbital weapons platforms. And with the Alien Abduction DLC, we know space based combat is doable (much to the chagrin of many). Would be a nice irony if the weapon needed to stop an invasion force (or some other threat) is the same one the Vault Dweller had to stop in FO3 Broken Steel.
You can put them in a gazillion places if you want to. A base in orbit, one underwater, another 5 miles deep in the earth, in a flying base (anyone seen new Bioshock's trailers? Whoa!). The question is, SHOULD you put them back? I, for one, think that they should be treated as they were in New Vegas. Broken, scattered and forgotten. A reference or remnant here and there is nice but a full fledged army will just make a lot of the fanbase go "not again!", and for good reason I believe. We nuked them twice already!
Wrong
Fallout- Avoidable
Fallout 2- Avoidable
Fallout:Tactics- Present
The Burned Game- Present
Fallout 3- Pidgeonholed into joining
Fallout:New Vegas- Devs lied, they arent avoidable.
But their role save F:T, burned game, and F3, they play no real role in the series beyond an extra slide.
IMO, the BoS are overrated, well, I like the East Coast ones, but all in all, their an annoyance in my opinion.
Fallout- Avoidable
Fallout 2- Avoidable
Fallout:Tactics- Present
The Burned Game- Present
Fallout 3- Pidgeonholed into joining
Fallout:New Vegas- Devs lied, they arent avoidable.
But their role save F:T, burned game, and F3, they play no real role in the series beyond an extra slide.
IMO, the BoS are overrated, well, I like the East Coast ones, but all in all, their an annoyance in my opinion.
They are avoidable if you follow Independent. Though who wants to do that when you can bury them alive?
In all seriousness, if the rest of the West Coast BoS is in the same situation as Mojave Chapter (NCR is growing, they're not.) then the Brotherhood is simply a goner. Come to think of it, something like "The Downfall of Brotherhood" could be good. They've been around since the first game. They deserve to go down loud.