My DM make a good argument to me about it last week in regards to mental skills:
You literally think differently. Your brain is made up of different brain-meats. It processes thoughts, feelings and knowledge differently. You don't lose knowledge about anything you know about but you think about it differently. Like that old episode of Transformers where Spike's brain was temporarily stored in a make-shift Autobot body. He literally didn't think the same way.
It doesn't affect proficiency, you're still trained to think better about that stuff (really why I liked the word "Trained" from 4E).
How you think is not the same as what you know.
Anyway I run a quick check of the MM (possibly missing some cases...) and found that monsters with proficiency in Knowledge skills include about a dozen creatures proficient in
Arcana and half a dozen proficien in
History (some in both). The only other knowledge proficiency appearing is
Religion, only Sphinxes have that. In addition to that,
Survival appears a few times, and it is ambiguous on whether your capabilities with it (finding shelter, food etc.) depend more on instinct or actual knowledge.
Therefore, on second thoughts, I think I'll always choose depending on both the situation (what you are trying to do or know) and the specific creature, if you allowed to use the creature's proficiency bonus, or if you are even allowed a check at all.
The general idea is you cannot turn into a specific individual. Maybe you can choose the
look of it, but you can't
be it. You assume the physical shape and capabilities (even magical) or a general specimen. But then it depends... if you turn into a Silver Dragon, I won't let you be proficient in History, I would rather say that Dragons know a lot of things because they have a long life span (in fact only adult+ dragons have this proficiency), but you
didn't live the life of a dragon, and neither you suddenly have all the knowledge of an "average" dragon. I can let you use the dragon's higher Int (in case of Polymorph), maybe that can represent a clearer mind to "connect the dots", but that's it.
Similarly, I won't let you turn into an Aboleth and gain "eternal memories", which by the way, are not an ability mentioned in the
stat block, it's in the "fluff section", nevertheless it's pretty explicit! I would say that you physically turn into a
possible Aboleth, but you weren't
born like that and lived its life, and so you didn't have any parent who could pass all the ancestors' knowledge onto you.
OTOH if you find a spell that would let you "enter inside the mind" (possess?) of an actual Aboleth individual, then sure I'd let you read its memories. But not with polymorph.
Again, I'd make it very dependent on situation and creature. Maybe I decide that Flumphs do not
learn their Knowledge, but just
know it, due to a deeper intrinsic understanding of things in the universe (maybe they "see across space and time"). In that case, I'd let you use their knowledge proficiencies if you turn into one.
Similary for those few cases of
Survival. I'd look it up if it seems that one creature is proficient as an instinctive ability (presumably all beasts) or because of its culture (e.g. humanoids). I'd say yes to earning the proficiency in the first case, and nay in the second.
All in all I guess it won't be often a problem. Most monsters are only proficient in
perception and
stealth, if anything at all
