I concur on the quest needing improvement. As it stands it's a cakewalk with a lightshow, and surprisingly little meaning either way.
Playing the quest as a good character, I felt short-changed about how ludicrously easy it was, and I couldn;t comprehend why exactly nobody else in the last 200 years had thought to take Mentats and disarm the Bomb, if they felt so strongly about it. Initially I thought it was because as a Vault Dweller my character had better technical knowledge, but then it was established that 'Dad', a technical expert with a penchant for selflessness and helping people whatever the cost, had also wandered through here - repeatedly - as had several other Vault 101 members back in the days when the Vault was open. None of them had thought to disarm the large nuclear device sitting about a quarter-mile from their own home, close enough that the Vault would likely be badly damaged by the explosion.
Playing as an evil character, I felt similarly short-changed by how absurd the premise is - while everyone else in town refers to me as 'the do-gooder from the Vault' (at least until I've lost a bit more karma), Burke inexplicably thinks I'm a better person to talk to than the fanatical cultists who also want to blow the town up - and that the best place to talk about killing everyone in town is in a quiet public bar. Worse yet, he wants the town gone because his boss made an offhand remark about it being ugly, even though being known as the guy who blew up a town for kicks is likely to get a fair chunk of powerful people, good and evil, out for your blood - Lyons wants to protect people, the Raiders want to *raid* people (big radioactive craters aren't known for their loot - well, The Glow aside), the Enclave regards the area as sovereign territory and would take this as an act of war - the list goes on. It's total nonsense as written.
While the quest, as it stands, has so many holes that more or less anything could replace it as a motivation, my 'take' on a revision would be this.
Megaton was founded around a convenient crater, because as Simms says, it was shelter from radioactive dust storms for the town founders. There was no nuke there (that they knew of) - after all, it would be senseless to try and shelter from radiation right next to a leaky atom bomb!
But, as with everywhere in the wasteland, clean water is a problem. A few lucky people have access to some small-scale distillers and can get enough clean water for a small group to live on, but the biggest obstacle to expansion is supply. Megaton is no exception, and couldn't initially grow much beyond two or three families.
Enter Alistair Tenpenny, a former wanderer and explorer who, as the game establishes, has become absurdly rich and can provide a small paradise to anyone willing to pay an exorbitant fee. To my mind, that suggests something - he found a G.E.C.K., probably only partly functional, and used it around Tenpenny Tower to create a little slice of paradise, and rent it out as his retirement package.
But, a G.E.C.K. was designed to supply a sizeable community from a Vault, so he has more resources than he needs, particularly water. His tenants can afford to live in absurd luxury, but still trade away significant quantities of water for caps, to trade in turn for other basic goods that they need - like medical supplies and spare parts, say. Tenpenny becomes even richer, not just from the tenants at the tower, but from trading water to all those nearby - including Megaton. Tenpenny effectively gains control over how civilisation reforms out here in the Capitol Wasteland, and he doesn't plan to give up that power. Of course, there are raider problems - but offer free apartments to anyone who's willing to take up arms and fight them off, and the problem soon solves itself (particularly added to the threat of destroying the purification equipment if the Tower gets successfully invaded - without water purifiers, it's worthless).
Then Vault 101 enters the scene and threatens to spoil things. It opens its doors, starts trading with Megaton, and when it finally shuts its doors, it has left several people outside the Vault as 'ambassadors'. These people have access to technology and expertise that the residents of Megaton don't, so they offer to start solving the basic problems of the community - sewerage, medical treatments, and water. Small scale water treatment is quite possible with the right know-how, so they set up a system for Megaton. Megaton breaks off its reliance on Tenpenny, and can even afford to start selling some spare water on to other travellers. Suddenly, Tenpenny's empire looks increasingly shaky, but there's not much he can do about it - Megaton's pretty well dug in, so hiring hitmen isn't much of an option (although he probably tried).
But, only recently, there's a twist. The water treatment system is very much in need of fixing by the time the game starts properly; it leaks, the water's increasingly contaminated, and it's in danger of a total breakdown. If it goes offline, Megaton's pretty much doomed. So, of course, Megaton starts preparing to expand its water production by more mundane means as a backup, and the first stage of that is to dig a new well, which is easiest (with their limited equipment now) at the bottom of the pre-existing crater. They dig down, say, ten feet or so, ready to - oh, wait, what's this big metal thing in the way? Is that a bomb in the middle of our nice little town?!
The Cult of the Atom, which existed in the town for quite a while and is perhaps the biggest faction in Megaton, takes over the project by threatening force, excavates it fully, and starts jealously guarding it. The more secular of the townsfolk are damned worried that the fanatics are going to find a way to set it off, or that some outside power will come along to take it away and leave no witnesses. They need a way out - enter the player, another Vault Dweller, with more advanced knowledge than the residents can muster. He/She is the best hope that the town has for disarming the nuke, in preparation for quietly dismantling it and disposing of the pieces safely before anything goes badly wrong.
Meanwhile, though, news of the discovery is spreading to the town's closest neighbours, and Burke (now virtually running the show with Tenpenny increasingly senile) sees a way to restore his employer's prestige - if Megaton should have a little 'accident' with its new discovery, Tenpenny's water monopoly is restored. It's also a warning to anyone else who plans to cross Tenpenny - mess with him, and he'll find some way to destroy you and everything you care about, and he's willing to wait years for the opportunity.
Quite apart from which, Burke is no fool and doesn't want a live nuke lying around for anyone to make use of. Two birds with one stone, you might say - and the only way he can gain access to the bomb to arm it for remote detonation is to ask the Vault Dweller to arm it instead of disarming it, as Lucas Simms wants - Tenpenny isn't a name that's welcomed by Megaton settlers, even fanatical cultists who want the same thing.
So, now Burke has an actual reason to risk his life trying to get the place blown up, Tenpenny Tower is no longer just some place that is nice to live for no particular reason, Megaton's residents may not actually suffer from congenital idiocy, and the reason the bomb's still there is simply that the other major factions haven't had much of a chance to hear about it yet, if the bomb was found in the last month or two.
Better yet, it also provides a potential motivation for completing the main quest if your character is evil - Burke and/or Tenpenny will be concerned that some guy is running around claiming to be on the verge of getting Project Purity to work, and finding out that you're his son - and that you're not averse to helping Tenpenny out - would prompt an offer along the lines of "Take control of Project Purity, run it in the Tenpenny name, and we'll split the cash". After 'Dad' dies, and the player can actually stake a good claim on the Project, it makes a lot of sense - and include options to betray Tenpenny and set yourself up as the Water King, naturally.
Unfortunately, I have no more than a barest modicum of computer talent, and little to no understanding of the FO3 construction kit; much though I'd like to for this myself, I'll have to wait for someone else's interpretation of the quest. Ah, well.