What exactly is the story of Fallout 2 is something there is a million answers to. When you've spent enough time looking at the code and the dialogues and replaying it, and you're being fully impartial and hold it in no high regard, it becomes obvious that this wasn't really intended. If you transported it to the Fallout 3 engine it would be worse than Fallout 3 was in most of the ways Fallout 3 is griped about (except the tastes the main story caters to would still be different, so someone might actually prefer it). If you transported Fallout 3 to Fallout 2's engine it would probably be very boring and generic.
Well, yeah... Fallout 2's very essence was the engine it was built on. That's part of what makes Fallout 2 a Fallout game.
Fallout 3, that was built with TES fans in mind while adding stuff to attract new customers. Their "storyline" was a fan service, and that's it. Transporting Fallout 2 to Fallout 3's engine would be like transporting Halo or Unreal Tournament to the Call of Duty engine. Those games have completely different playing styles, yet if someone was stupid enough to make the transfer, they would be pretty damn boring and bland. That's because they weren't MEANT for that kind of gameplay on the other engine. Fallout 2 was never meant to be in the first person, even if they had the technology to make it possible. Fallout (1 & 2) was made with tabletop roleplaying, isometric gameplay, and turn-based combat in mind. Fallout 3 was made to look and act like TES, but put in the Fallout's world.
Let's take the VATs system in mind for example. Horrible fucking system. Yet it was made as an attempt (albeit a bad one) to reconnect Fallout 3 with Fallout's turn-based routes for people who didn't want to play a first-person (or even third-person if you change the horrid camera control view) game. There's a REASON people don't like fallout 3, and some still barely tolerate Fallout: New Vegas even though it was made by former BIS developers. Fallout 1 and 2 was not meant to be that type of game (by that type of game I mean Fallout 3), plain and simple. Let's pretend, just for a moment, that Black Isle Studios had the same technology as Bethesda did at the time of Fallout 1's creation. Even with said technology, the game would STILL be isometric, it would STILL hold a world map, it would STILL be turn-based, and, well, it would still be a "Fallout game". BIS didn't incorporate many things that Fallout 3 fans seem to love because that's not the kind of game they wanted to make. These guys wanted to make a genuine RPG, like the one's before computer games were a public hobby and RPG fans had to play on a piece of paper with a pen, however they wanted to bring their visions to life on the computer while at the same time keeping the core essence of the First-Generation RPG (as I like to call it). Sure, maybe they couldn't have gave everyone a talking head or get a voice cast to voice every single NPC in the game. But there were things Bethesda couldn't achieve that BIS did. Take the sizes of towns in Fallout 3 for example. After 200-some odd years of regrouping, humanity still can't manage a town with more than a couple dozen citizens. Get the hell out of here. Call it technological limitations or whatever, but BIS was able to achieve their vision pretty much exactly the way they wanted it with their technology, yet Bethesda could only achieve half of their original vision with their supposed "superior game engine".
It's almost like how the Grand Theft auto series decides to recreate their universe and wipe the slate clean everytime their game engine makes an advancement. You have the 2D universe (GTA 1-2), 3D universe (GTA 3, Vice City, San Andreas), and the HD universe (GTA 4-5). That means everything that happened in San Andreas, never happened in GTA 5. Yet many of the same things appear in both games, such as city streets and names, gangs, etc. Now, if one was to compare Fallout 1-2 with Fallout 3 this is how it should be looked at. They were obviously meant to be two very different games, only brandishing the same title.
Fallout 1, for example, held the "world map" as it did not completely because of technological limitations, but because it was trying to show the players how Southern California had been turned into a barren wasteland, with scattered settlements several days journey away from eachother, with nothing but mutated animals, raiders, and the occasional trader in between in the vast expanse of the desert (keep in mind I'm leaving New Vegas out of this for a reason). Fallout 3 however, pay's single attention to one area, yet, these settlements are anything but several days journey from eachother. It gives a cluttered feeling, while Fallout 1 gives you the true view of a post-apocalyptic nuclear war.