This is so subjective. Everyone has their own nemesis.
I finished my last ATPL exam a few days ago.
You can split everything into 2 groups: Group 1) Which subjects are difficult to study/ understand, and Group 2) Which exams are the most challenging.
To study I think universally everyone is split between either Met or Gen Nav. Most people struggle with those two.
Personally, I found Flight Planning to be the most challenging exam. To study it's very easy but in the exam you are pressed for time and there are plenty of questions which can trick you. I actually scored 100% in this exam but I still maintain that it was the most challenging exam out of all of them. For me at least. Everyone is different.