This may not be a helpful suggestion.
If by "the original developer's intent" you mean Microforte's intent, that will always be a difficult road.
Instead, how about a mod that undoes many of the issues FOT had with setting and canon, taking over from the end of FOT? In effect, dismantle the FOT setting piece by piece, and leave behind a Fallout setting.
A basic outline could go like this:
* Assume the Warrior destroyed the Calculator. Then he just...wandered into the sunset, or something.
* You are a very fresh recruit from Brahmin Wood. Toward the end of the Calculator War, new conscripts were being fed into the conflict as cannon fodder. You start the game in the medical tent of Camp Epsilon (I know they call it a bunker, but...it isn't).
* Most of the Brotherhood is dead, so maybe it starts like 28 Days Later, or Torment, where you've just regained consciousness.
* Finding that the Calculator is dead, and not-a-Vault Zero is wrecked, you decide to go back to Brahmin Wood. A few other Brotherhood people want to travel back to their homes, and they are your party. Along the way, many of them return to where they came from.
(* Talking hairy deathclaws suffered a 100% casualty rate. Not an outline item, but a desirable detail.)
* Along the way you find that, despite all that the Midwest Brotherhood accomplished in such a short time, everything is falling apart. Former allies are fragmenting, there are Brotherhood internment camps to be liberated, warlords, petty states, banditry, and so on. Bunkers have been destroyed. Some Brotherhood people have "gone native", or insane...even a bit of "exterminate all the brutes" might be permissible.
* Generally, the wasteland is returning to something more like it's pre-Brotherhood state.
* There are also newfound ideals, commerce, and a technological renaissance, but these are the exception, not the rule.
This can free up the setting, explore interesting factions, etc. A practical side benefit for an ambitious mod is that you could re-use existing maps, though you'd want to modify most of them somehow.
It would also dilute the tendency to create huge political and military forces going head to head against each other. They may have their time in the sun, but...it all ends in tears.
Which is as Fallout should always be.
(It turns out this wasn't a suggestion at all, it's a manifesto!)