You know you could have saved when you got through, let yourself get caught, then run to the library, right? Writing up those quotes and numbers, reset, and voila. A lot less time lost.
Anyway...game-wise there were only a few moments that got me. The first one was that goddamn garchomp, mainly due to being unexpected (and having no clue how to take down such a thing). It took me quite a lot of time and money to defeat him (and a bit of luck, too).
Next up is the chrysolia forest. What a mess. Following were those cult guards, especially since I didn't know there was a library where I had to go first...(had a quick solution to that, eventually).
Finally, that tedious web puzzle in aventurine. I NEVER WANT TO DO THAT ONE AGAIN. NO.
Honorary mention goes to the Aster/Eclipse double battle close to Calcenon. Rendering my EQ flygon useless with HP ice on magmortar among others, dammit. That was one tough double battle.
Story-wise...I'm not going to begin on that list. It is very well written to make you rage on purpose (in a good way, Ame where are our Fern Voodoo-dolls?)