Bullseye said:
do something with the encounter with the aliens (fallout 1)
Technicaly a good idea.
Another thing is that there are a lot of keys in fallout 1, but you can't use them some quests would be handy...
The last thing i'd like to suggest is a big fat bonus for killing everyone in a town (i love to do that

), the most fun thing i would like to have is that after killing everyone in a town you could sell the town to a group of raiders or something (and after selling it, killing everyone again, hehe). that are about all the ideas i have atm. only thing 1 thing is left, the glow. I love the glow and i think it would be really cool if you had more things to do there.
If someone might think "why doesn't bullseye talk about fallout 2?" there is a plain reason for that: i might suggest something wich is already in the game, i didn't do everything in fallout 2.
Didn't like this that much!
Anyway:
Whatever the quests are, they should be really rewarding. Not just caps, stims, exp, etc...
Something unique.
Something special.
Something, that gives you the opportunity for other quests.
What about tech raiders (hackers) which have their base at an old Vault Net Control Building/Vault or so? Like an "EVIL" counterpart to the brotherhood.

They have even more theoretical knowledge than the Brotherhood, but they are unorganized, lack in practical skills and have no equipment to develop such technology.
You could do some jobs for them, like stealing from the brotherhood, killing guys, this might add new quest for the brotherhood and give the many (useless) brotherhood bases in F 2 a sense. (you could steal there etc.)
Of course there should be a way to make everything GOOD or BAD or TOTALY FUCKED UP at the end.
1. Good way: You make the raiders and the brotherhood work together, so the brotherhood gains it's strenght again and make the wastelands a better, safer and cleaner place.
2. Bad way: You can make the raiders fuck up the brotherhood.
3. OMFG way: You make the raiders sell themselves to the Enclave, which gives them new technology. (in such a case, you have to destroy navarro in 30 days, or the enclave is gonna attack EVERY town in the wastelands and they fight against the brotherhood paladins and supermutants, guards and citizens.