Post Chemical Plant spoilers
And finally 2/3s of the way through the story spoilers
Also, make sure you visit the GCPD after every major plot point in the story. The amount of different dialogue that has been recorded is astonishing. Head to the evidence room as well, lots of cool stuff in there from the previous three games.
I'm also glad they acknowledge the events of Origins, considering it wasn't a Rocksteady game they could have quite easily ignored it.
They did an awesome job this game with gong back and mentioning stuff from all of the other games in the Arkham series
First spoiler
Second spoiler