I'd like to add to the puzzle difficulty discussion: Don't think about them in the context of gameplay, think about them in the context of the story, Nate usually puts the pieces together because he has vital information that is needed to solve them. I mean try solving them without using the journal and skip all the cut scenes, you would have to be extremely lucky to solve them like that.
It's the same with every profession, a mechanic has better understanding of fixing cars than a plumber because he has studied for years how to repair them. Now Nate knows Latin, history, religion, and archeology, solving these puzzles is his profession, the whole point is that he can solve the puzzles that others can't as long as he knows the context, in the game's world he has spent years studying these things and it has to be shown somewhere.
