A good idea perhaps would be if they had used the Virtibird plans to make an aviational vehicle of their own. With that they could supply high level transport for traders and such, though I think they should be set within an area, like the regions surrounding thier main base. BOS are good to have around, but no everywhere. For example you could have 'bad lands' and such, where the brotherhood dont patrol / exist and where bandits / other powers rule the roost.
BOS deffinatly need to make an appearance, but there presense should not be overwhelming (a la craptics). It would be awesome if you could join the brotherhood once again, like in F1, but I think the mission should be MUCH harder than the "run down to the glow, grab disk, run out" mission which they set in F1. Perhaps the player should have to complete a serise of 'favours' for the brotherhood just to gain access to the outer areas of there facilities, and they they have to proove themselfs further to actually earn the right to go deep into the depths of the brotherhood, and get power armour.
I think the main reason the Brotherhood played such a good role in F1 was because they were the only guys with power armour. I think we should see a repeat of this, unlike in F2 where power armour was abundent as soon as you reached San Fran.
Things that will be cool in F3 (And I say will be, because its bound to happen) would be to see the power armours get a buff and look even more badass than before. I didnt like the power armour in FOT, the spikey look really didnt fit with "the ultimate armour" theme.
Perhaps have the old (original) power armour avalible in a few places, and have the brotherhood using some sort of super advanced power armour. Anyway, I am just throwing ideas around, it would be awesome IMO to see similar themes in F3.
The Brotherhood DEFFINATLY need to own the best bad ass armour, that what made them so awesome in F1. No one else had access to such devistatingly powerful weapons or armour than the brotherhood.