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I agree to an extent, but this could have very well been an item that is undetectable by such skills. I am sure you remember various modules in AD&D where a given item was an "exception" to the skill system and required special checks only available to the module or a given situation (ie a charm check to get the person to tell you).
Don't get me wrong, I would love to see layered skill applications as you mention, but there are sometimes where the GM takes liberty in the story in order to preserve the surprise.
My pen and paper games where comprised of engineers, physicists, chemists, etc... if the GM were entirely confined to the rules of the book specifically, the games would have ended up quite boring.
Sure. Just more options to use the stats of combat is always cool. Always seems that games focus so much on combat that you don't get a lot of reasons to develop non combat traits. DOS seems to be doing pretty well with that in general.