In brief, what I thought you were saying is that skills like carotgraphy can easily be rendered useless with multiple playthroughs unless the designer makes randomly generated maps and so on.
What I was saying that you can argue this for every skill in every game and thus it becomes a (mostly) moot point.
You cannot argue that without becoming patently absurd. Most skills on a computerized RPG are centered around combat; if it has skills at all. Even without, the class structure still recognizes those with combat skills, and how good they are (the fighter class, higher levels, etc...)
Cartography is on no way, shape, or form on par in usage with any combat skill, magic skill, or thieving skill. It is a utility skill; and a passive one at that. Many games do away with it entirely (Wiz8 for example, Bard's Tale 3, Might and Magic VI/VII, Baldur's Gate...). THAT tells you it's importance.
I find it on par with language skills. It's either useless, or it's not. There is no middle ground where it's 'sorta' useful. It either gives you complete enough information, or it doesn't. Not many skills are like that. In fact, other than language skills (which are very, very, very rarely used at all in computer games), I can't think of one less used.
Push come to shove, I can easily hand draw the maps. Wouldn't be the first time, as the sheafs of old graph paper with hundreds of maps sitting in my file cabinet can attest.
That Power Armor, that sword, are examples of either bad design choices, or choices made specifically to give players a VERY easy way to victory. Which is, IMO, a bad design choice (compromising the entire design just for those who cannot, in any case, complete anything more difficult than Pong).
Whats more, that sword should have been made worthless by virtue of the absence of skill with the sword. The Ultimate Sword of Destruction is still a sword, and from experience, one does not just swing a sword like a bat! Real swordsmen will quickly eviscerate you.
If the game is non-linear, then it should be built to handle things such as the player going to places the designer thought should come much later. If it is imperative that the player not go there, find a way to prevent it. Have the town under lock down, and needing a password to enter, or have them need to be certified Crusaders. Write around that instance, not ignore it and hope it doesn't happen (because it will).
If not, then it's bad design. You can note my statement on character death to see what I mean; the story should be written to adjust for eventualities such as a key character dying to a level 1 trap, or instead of going to Ankh-Morpork they went to Skara Brae.
Quests cannot be argued in this manner with any sense of logic or sanity; quests are simply objectives within the game. Some may not have anything to do with the main plot, some may. Without objectives, it's a sandbox with people running around butchering anything that moves with no real motivation, and it becomes Halo instead of an RPG.
You're confusing tertiary skills with primary; and somehow managed to blow the entire thing out of proportion.