The worst one for me was the unexplained significance of Lake Silvertear in Mor Dhona.
Hydaelyn tasked Midgardsormr to protect it and he did for 10 000 years.

But we never really explored what was the deal with that.
There's a 1.0 trailer showing the ARR primals popping out of it but that's it.

And with Hydaelyn and Midgardsormr gone, the two people tied to that plot are gone.
The only hope i have is for the Alliance Raid to mention it, considering we go to the gods realm from the lake.