These are what we call the 'YMMV items.' Things that some people find in this work. We call them 'your mileage might vary' because not everyone sees these things in the same way. This starts discussions in the trope lists, a thing we don't want. Please use the discussion page if you'd like to discuss any of these items.
Percy, the head of Division, at first seemed like an Affably Evil character who was Only in It for the Money, working for Corrupt Corporate Executives and criminal organizations just as easily as for the government. However, as the series progressed, we've seen just how far he'll sink to achieve his goals, including murdering the loved ones of his own agents to keep them loyal. Perhaps the most shocking example of this was the revelation that the terrorist who killed Michael's family was, in fact, a Division agent who did so on Percy's orders so that Kazim Tariq could be Percy's mole in al-Qa'ida. When Kazim accidentally killed Michael's family instead, Percy recruited Michael with the promise of getting even.
Amanda is also a Complete Monster and a Manipulative Bitch who constantly and ruthlessly tricks people into doing what she wants and earning their loyalty (or at least their fear; she's quite Machiavellian). But more to the point, she's the resident Torture Technician and is quite skilled at her job, using everything from electrocutions to breaking bones to threatening lobotomies in order to get information out of her victims — and it's quite clear she enjoys doing it. She's the one person Nikita is afraid of.
Critical Research Failure: LHD vehicles in Hong Kong. Least they got parts of the HKPF uniforms right, except for the uniform jacket.
Michael "asks" if his attorney was called in from the US Embassy. While this may be false since Hong Kong has a US Consulate, it can be possible for a lawyer to be placed in based from the word of the US Embassy.
If there was any doubt as to Percy's qualification, it was no doubt removed as of episode 1x21, "Betrayals", and his status is solidified by 1x22, "Pandora". This man could give LionelLuthor a run for his money.
Amanda as well.
Moral Event Horizon: Well, Percy crossed it a long time before the show began, but in-series he crosses it when he kills the Engineer for becoming obsolete. Note that Birkoff was visibly disturbed when he witnessed that.
And if not that, then altering the agent tracking chips to also be kill chips may also qualify.
Actually, screw both of those. His true MEH was The Reveal that he's the one who had Michael's family killed, so that he could recruit Michael into Division.
And then it turns out that the plan was for Michael to be killed, building the rep of a Division mole, allowing him entry into Al-Qaeda. When Michael survived, Percy recruited him into Division with the empty promise that they'd hunt the man who killed his family.
Amanda hits hers when she deliberately provokes a bad guy into killing one of her captured agents in order to get Alex to go.
And any moral points she still had left go out the window in "Fair Trade" when she nearly lobotomizes Birkhoff.
The Scrappy: Ever since the first episode, Jaden has been consistently annoying both to Alex and the viewers.
And in real life, there's "Shaggie" for fans of Shane West and Maggie Q being a couple.
Seasonal Rot: The drastic changes to the show's setup in season 3 were not welcomed by the fans, as well as several unpopular plot twists that caused the ratings to drop like a stone until the following season was not only the last, but given just six episodes.
Tear Jerker: Alex's flashbacks after her panic attack, and the reason why in the fourth episode.
And Alex shooting Thom and breaking down in tears after that.
In the season finale, Alex calls Nikita out for her obsession with taking down Division, and using her. You can practically see their relationship fall apart on screen as Nikita tearfully tries to justify her actions. And the worst part is, we'll never know if it would have worked, since at that moment an assault team attacks the loft.
Villain Sue: Percy has a lot of these traits. He is almost never unnerved, he always has a back up plan, and even when Team Nikita wins the battles, he most often wins the wars. However, this has finally been averted at the end of season 2 in "Homecoming" where he meets his demise at the hands of Nikita. Literally. She drops his ass down a shaft and he lands in the prison Amanda used to keep him in. Karmic Death indeed.