I can't say I'm sorry to see that douchebag Jai Wilcox gone, but I wonder if Arthur Campbell was behind the bombing instead of the weird group Jai was apparently sponsoring with a Big Dipper-y tattoo as their signature.
Also, the new boss Annie has is... interesting. She basically encouraged Annie to start sleeping with her assets to distract them from what she's really doing. :O That's a pretty bold step from an agent who originally wasn't even field-qualified to use a weapon until about midway through Season 2!
I think Arthur was behind getting rid of Jai because Jai was a giant dick to him at the end of Season 2, and him boosting Auggie into the slot Jai used to have is a way to gain control over a rogue organization within the intelligence community.
Also, finally: I loved all the A-squared moments! SQUEE!
(Have you seen Auggie's chest? Dayum, dude's hot.)
(Also, Annie in her training outfit? Also hot.)