The Chris Carter Effect: As the second season has progressed and more characters are introduced or revealed to have their own agenda, it's 50/50 whether week to week things are being thrown at the wall and seeing what sticks or if there's a master plan and the series is falling into this or Gambit Pileup.
Designated Hero: Kiera, who starts off as basically A Nazi by Any Other Name, though a very sympathetic one. It doesn't help that, for all her trying to do the right thing, at the end of the day all she cares about is getting home, which is impossible.
Jerkass Woobie: Kellog seems to be a classic Con Man, Manipulative Bastard and Punch-Clock Villain abusing time travel for his own gains. Then he had to watch the woman he thought/might be was his grandmother die in his arms due to his former comrades trying to blackmail him and his own back story implies he only joined up with Liber 8 after he was wrongfully arrested because he stayed with his dying sister (the real Liber8 member at the time) in her last moments when the arresting officers fired upon them it is really hard to not feel bad for the guy. And he gets to witness the Charlie Foxtrot that the Liber 8 inspired timeline becomes, as he becomes one of the last holdouts after a series of devastating inter-corporate civil wars.
Foe Yay / Les Yay: Garza for Kiera in a kind of weird one-sided way. Along the way she also throws a smooch at Fonnegra. Then again, she likes trolling Kiera, who seems a bit straitlaced in the realm of sex.
Kudzu Plot: Season 4 developed into this. The Gambit Pileup of Liber 8, the Traveler, Future Kellog's Commando's, Kellog, Theseus, Kiera, and the VPD, with loyalties and motivations changing per episode, it became incredibly frustrating to follow. And it only lasted 6 episodes.
Moral Event Horizon: Even though the entire season was building up to Green Alec being evil, it could still have been argued that he was at least well-intentioned. Then comes the season finale, where he taunts Red Alec by claiming that he will do everything in his power to keep Red Alec from being happy with Emily, even if that means killing her, and uses his dying breath to rub Kiera's lost family in her face. Even before that, he tries manipulating her by mentioning her lost family.
As far as Kiera is concerned, Green Alec has crossed this line by the time of 3x10 "Revolutions Per Minute", by cutting Green Kiera's CMR out of her corpse and using it in Halo.
Paranoia Fuel: Quite a bit of what Liber8 is fighting against is disturbingly plausible. And some of it has already happened. Kagame explaining how the banks dodged responsibility for the 2010 crash is a good example.
Seasonal Rot: While things were getting a little murky come the second season, it still managed to attract fans and keep telling a relatively compelling storyline. Season 3, however, is where most fans agree the show really started falling apart, with many plots seeming only half-developed or rushed, and everyone turning on each other at the drop of the hat, making the heroes and the villains pretty unlikable for once. It also doesn't help this season decided to play heavy with a time travel plot to Ret-Gone the ending of Season 2 and played up an obvious Evil Twin plot with Alec. It's also a major sticking point this was the season that caused the network to cancel the show, approving just one more mini-season (only 6 episodes) to wrap things up. However, as much as Season 3 is disliked, it did give the series a decent ending with, which only became a Series Fauxnale by the final scene. Then Season 4 came along and basically through the character's growth AND all of the carefully established rules of time travel completely out the window. Basically, while Season 3 is not beloved, Season 4 is reviled.
Special Effect Failure: For a show that usually has decent special effects by the network's standards, the completely CG power-armored future soldiers pursuing Kiera in the fourth season opening look laughably bad. It's especially jarring given how good they looked standing still at the end of Season 3.