My problem with Season 2 (spoilers ahead)
first of course: Recast of Adar. I read they had to do it because the actor wanted to leave.
bad decision.
second: the balence of the different stories. In the beginning it was quite balances between
Gandalf - Elves - Dwarves - Numenor. Later we don't see the Gandalf Story at all for one episode it also does not effect the other stories (yet), we dont see Elrond/Galadirel one episode. You always think - how can the elves write a letter to the dwarvs so fast, and Elrond and the elf king still dont even know that celebrimbor made the rings. or that he did not receive the warning.
for me the dwarves story was played out best in the second season.