Skills that interact directly with quests, like repair, are always 'non-systemic'. At most, they have a systemic secondary effect (like for example, preventing weapon jamming).
What, did you want to use repair or science to check all broken computers in the game for finding a randomized voice module?
Quests don't need special treatment of skills unless you want to employ skills which make no sense outside of special use cases. What I mean is that science is such a broad and abstract name of a skill that it has no use apart from certain special interactions with gameworld objects. If you take Deus Ex as an example, there's Electronics and Computer skills and they both have very systematic uses. With the help of level design both can be used without the need for special handling to progress through the levels. They can provide you extra information or extra access routes, extra items etc. If every functioning computer in Fallout could be interacted with using the science skill and this interaction would in majority of cases provide something meaningful then it would be systematic use and at the same time some of the computers could provide some quest specific info, or whatever. In reality there are probably hundreds of computers in Fallouts and only a tiny portion of them does anything meaningful and the only way to find out is try.
In Fallout several skills do nothing on their own and the devs need to make a per specific object script for the skills' usage and then if they want a solution to a quest involving an interaction with a computer they need to place the computer and make the scripts. What I'm proposing is that they make a skill which itself systematically handles the interaction with all computers and when they want to do a quest involving computers they just add a computer and decide how will the interaction proceed. And if they wanted even more systematic approach, all computers of one type would have the same sort of interactions etc. This problem can be seen in other areas as well - many games have hundreds of NPCs, but only a chosen few can be talked to or have hundreds of dialog options, but only chosen few are affected by your speech skill, etc. I would like to see a game where instead of trying to find those few important NPCs that can be talked to, all NPCs would have at least some basic dialogs allowing you to ask them for directions, information on some topics, etc (yea, Daggerfall, except more options and more meaningful info gained through the conversations). And instead of a couple of [Speech 40] dialog options I would like to see a more complex dialog system taking into account such things as character reputation, relations, and possibly many more things. Ideally, but that's a very distant future, games could generate whole dialogs based on some attributes of the character, which would allow having some sort of meaningful dialogs for all characters in games with many characters without requiring huge amount of work.
Also I would much prefer if Fallout told you which objects could be interacted with using special skills, but it seemed that they expected the player to come up with the solutions just like in most adventure games. Often it's just using random skills on every object just to figure out if they do anything special, which in most cases they don't.