In my very first playthrough I simply missed the Mine in Broken Valley where you can find the Crystal Skull ... It's even more funny since I was all the time (that first playthrough) confused when I hear two NPC's talking about the Mine in the Black Boar Inn and I was always thinking they talk about the Mine quarter (the place where you can find Williams) ...
I was totally confused ... :haha:
2) I also missed the Forlorn Cave, a nice one with a funny quest for the two sisters ...
Missed a few skillbooks first time (Farglow, Black Boar Inn etc etc ... )
And to know I play all rpg's "thoroughly" ... but I love it to search and the game secrets are well hidden !!