The Fifth Column leader and V doctor, Joshua. He can easily be seen as the most heroic out of all the others rebelling against the Vs because he has the most to lose. When it looked like he died in the finale, many fans wanted to drop the show entirely, but He Got Better by the end.
Lisa similarly is well-liked; surprising since she is usually in scenes with The Scrappy Tyler.
Family-Unfriendly Aesop: The people who mistrust the supposedly benevolent aliens who want to keep us all healthy for free (universal healthcare), give us a replenishable source of energy (removing our dependency on oil) and just generally want to make the world a better place while showing no signs of bastardry ARE RIGHT!!!
Follow the Leader: Arguable, the BSG parallels are noticeable, but it's more the concept of the reboot (an old Sci-Fi series reworked for greater political relevance and additional religious themes) than the core pitch of the shows themselves.
The corridor where Live Aboard subjects are taken.
The face melting scene in the opening minutes of Season 2. Jesus Christ. The fact that it got by on ABC uncensored is incredible.
What the Visitors look like underneath their human guises. Granted, some of them are on the side of humanity, but still, you wouldn't want to be alone in a room with one of them sans their human form.
Anna eating a mouse. Whole. And then she proceeds to feed to Ryan's daughter mouth-to-mouth.
Definitely the skinning of Sarita Malik, Visitor sleeper agent - especially when Ryan pulls out her REPTILIAN tail. Yikes!
Paranoia Fuel: This trope looks to be the remake's bread and butter. Not only do the humans have to worry about anyone being a Visitor, but the Visitors have to worry about anyone being part of the Resistance, even other Vs. It gets even worse in "It's Only The Beginning". You know that swine flu cure that everyone's been so desperate to get? There might be V chemicals in there that will eventually turn you into a mummified, desiccated corpse.And there's no way to tell if the chemicals are present or not.
Except that's just what you're supposed to think. Instead, what they really do is implant some sort of tag into your DNA that is completely undetectable to human technology. The tag constantly transmits your location, physical condition, and more to a database on the V ship. And there's still no way to tell if the chemicals are present or not.
It goes even further downhill. If you try to raise a resistance against the V, not only will government agencies armed with alien tech hunt you down, but humans will too. Humans willing to kill. And you have no idea who they could be.
Tear Jerker: You can't help but feel for Agent Malik as she dies from torture. She even cries, which is a human emotion.
The Scrappy: Tyler. Even allowing for the fact he's a teenage boy, he's stupid and blinded by hormones. Doesn't help that he's dating Lisa (Laura Vandervoort). The feeling is largely based on his oh shiny sexy aliens expression mixed with the whiny "The Vs are awesome, you just don't understand me" thing he's got going. It certainly doesn't help that he's so much of an Unwitting Pawn that he's falling for plans that didn't even have him in mind, despite his own V girlfriend secretly trying to save him from what is surely an unpleasant death.
They Changed It, Now It Sucks: A number of fans of the original 1980s series complained that the lack of Nazi symbolism in the re-imagining ultimately leads it into losing the overall meaning behind the V's intentions.
They Wasted a Perfectly Good Plot: Tyler. He could have been an interesting character if the writers had used him properly. Instead, they make a character who is a 10-year-old boy in an almost 20-something man's body. He perpetuates the stereotype that young people are just destructive, self-absorbed, stupid, whiny lemmings. He served no actual purpose in the show at all. If he had been done properly, his death could have been shocking and horrible. Instead, it caused feelings of celebration, relief, a feeling of "You had this coming to you and you deserved it", and a feeling of "You reap what you sow." Yes, the writers made Tyler that bad. Such a terrible waste of potential.
Uncanny Valley: Intentional. The mothership-based Vs are presented through a glaringly obvious CG filter to make their skin appear too flawless and plasticky, and Visitors who are inexperienced with humans are a bit stiff and emotionless. The later becomes a plot point in the 6th episode, when Anna comes up with a test to use this emotionlessness to separate loyalists from Fifth Columnists.