I was surprised that they had a 2 hour finale, but was happy because the first hour was basically giving Callen a reason to shoot the Chameleon. I wasn't really that sad that they killed either of the two agents, I didn't even know the first one, but I felt like there was a weird moment when Hetty was speaking to Hunter's ghost that reminded me of a scene in NCIS with Gibbs where he was talking to his deceased mentor, Mike Franks. I was really hoping for more Kensi/Deeks moments, but that's because I started watching the show because of them, although all the things he kept trying to do to cheer her up was pretty cute.
The ending, ugh the ending was just miserable. I'm glad that the Chameleon is dead, but I really wish that Callen had just shoved him in the truck, drove off, and shot him where there wasn't a live news cast taping everything! Now I don't think Callen will be able to go undercover for a while, and if he does go to a federal prison the inmates are going to know he's a cop.
I'm hoping that Callen comes back as an agent, Hetty changes her mind and realizes that her team needs her, and that they go back to catching the bad guys.