Well I must say that I doubt this will happen as there appears to be little progress, but I'd have to say that bhlaab on page 1 had some great ideas. Feasible too!
What I'd change:
A sensible beginning? the growing up was a great training session, but waking up and "ARGH! everyones after you run! You're dad ran away and his buddy is dead!", please, this was the most disjointed part of the game. James wants to leave so they shoot whatsit and then deside they're going to hunt you down and baton you to death? where did that come from?
I'd handle this by increasing the number of radroaches and throw in a yao whatsit in the vault entrance (have it open still and jammed) and that chap who's meant to be dead is hiding in a locked room waiting for help.
The Vaults in anarchy, but they won't attack you, the guys are only after the roaches, the overseerer wants to see you, but if you enter the maintainance room or leave the vault without seeing him they'll go instant aggro on you. Talking to the overseerer he'll ask what you know, why it's happened, accuse you of plotting against the vault and you can take it three ways, you can lie and admit you're in on it (aggro), convince him you know nothing - neutral, or protest innocence and get that repair chap in bother.
Basically James left, but in doing so he jammed the door and the only way to fix it is with the console in the maintainance area, (optional quest), the roaches and bear thing ran in while that repair chap was trying to fix the door.
So when you fix it the overseerer will thank you if you're on good terms and let you come and go as you please.
The game needs more methods to find James really, so different mini quests for details, maybe play with the regular method and take out the GNR method, instead have the GNR as a stand alone quest etc.
Really I feel the plot should go:
James leaves the vault - radroach infestation
You hunt for James via clues
You find James, he goes to the memorial.
You talk to Doctor Li, have to quest for her and prove the project is worth while etc.
You get to the facility and find out you need the GECK.
You go get the GECK (NO ENCLAVE CAPTURE!!!!)
return and there are a few methods it could go from here:
a) Enclave attack and kidnap James etc, they want him to help them with a supermutant problem etc, ie recreate that experiment, but with the FEV, you can save him or help him there etc.
b) It looks like it should work, but they need better parts, You can then wander and find bits, buy them or chat to factions about it, like BoS has some parts and knows of places that might have the rest. Talon could have a part. Enclave has the lot, but you have to get into Raven Rock etc.
You build the Purifier and turn it on, you DON'T die! James made the purifier work without mass genocide. You could have it so James dies setting it up I guess, like placing the GECK etc in the water etc.
I believe some off-shoot quests would go down well, like reuniting the BoS, convince them to leave, cure ghoulification at underworld, start a war between BoS and Outcasts, pimp the enclave to towns etc.
Another annoyance should be sorted however, lamplight shouldn't be the source of the thousands of SM, i mean COME ON! What about the enclave? Granted they want to cleanse the wastes, but what if they were making a SM army and it went wrong? Where are those kids coming from too? should that go in that vault? like a human cloning project similar to the Gary vault? Only not insane?