The following rules, chapters and notes can be ignored/changed if you want a strictly more "Fallout" feeling. Technically, you can choose to ignore most of the rules except the more core and vital ones (go figure which those are.). Those are the ones seen in game for most Fallout games. But as said, you can pick and choose whichever pages you want to include or not (apart from the core), or change them slightly to match your taste. However, if you remove all but the core, then well. You might as well just play Fallout: The tabletop RPG and replace "human" with "pony". Althou, it lacks the rules for magic, flying etc.
Wisdom was added to have a second mental attribute, reflecting that despite being smart, you could lack experience. (Like the classic "barbarians doesn't need intelligence, but wisdom is required to be a good leader") Wisdom can be changed to Intelligence if so wanted, making it entirely "SPECIAL" once more.
The whole talent tree section can be ignored if you so please. This will technically make the characters weaker, but would add more to a fallout feeling of being "only human(pony)" to it.
These works pretty much like faith points in 40k. Just with a different flavour, and they are stronger the more friends you have in your parter (up to a certain degree). If you want to drop the whole "small miracles" things such as burning a point to not die, then feel free to. It just adds more caution for the party, knowing they are just fragile little ponies, in a big harsh wasteland with no supernatural (*cough*besidesmagic*cough*) powers to aid them.
As stated above, most skills can be removed for a combat only focused RPG. And merged for simplicity. Small guns can be made into a single skill without the sub-skills. And two other examples are "first aid" and "doctor" can be merged into "medicine". Intimidate, diplomacy, bluff and seduction can all be made into "speech". Doing this however, cuts your trained skills down to 3 (4 for EP).
Degree of successEdit
This being another additional rule, it can be used on it's own, to replace conditional modifiers, or be removed in case of conditional modifiers. Unlike most of the others, this one has the least effect of them all. In theory, it can be utilized to play a quite big part of it all.
In quite several RPG's, your character can't get tired or exhausted. If you cba to keep track of your characters remaining stamina, then skip this rule and just go with "unlimited energy".
Unlike many games (and Fallout itself), your character has a sort of "mental stability" pool in this RPG. Doing things like peeking up from cover when someone is bathing said cover in lead is not something anypony with common sense would do. So a will save is needed to do so. This rule can be ignored if you want to play completely jaded characters with no self-preservation instincts whatsoever. Like the common action hero.