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.
Simon and Blake Sterling are quite well-loved by fans.
Vicky also appears to have become one, seeing that Taylor Cole is drop dead gorgeous and her character is fairly complex. She evolves from a fairly flat evil character, to a Dark Action Girl with some sympathetic traits, and after the hiatus and retool has undergone a Heel-Face Turn and more or less taken up position as the female lead. Being Ms. Fanservice probably helps too.
Fridge Logic: If Sophia's people were able to transport their entire planet away from the supernova and near Earth without simply destroying both planets, why did they have to rid Earth of its population? Why not simply live permanently alongside Earth?
The planet appears to be in pretty bad shape. The real question is why they think they need to kill most of the humans to make room for a billion aliens? That's less than two decades of human population growth. Just put them in Central Asia or Canada.
Growing the Beard: The two-part Inostranka breakout episodes, which saw the end of the show's tendency to show dozens of flashbacks per episode. After the hiatus, many viewers who had given up on the show beforehand flocked back to it in droves. Unfortunately, not enough of them came back to save the show's plummeting ratings.
Hilarious in Hindsight: In the episode "Face Off", Sophia's people use their portaling technology to cause a massive earthquake which destroys the Washington monument. In August 2011, just a few months after this episode aired, there was an earthquake in Virginia - the first of its magnitude to hit the East Coast in over a century - that caused cracks to appear in the Washington Monument.
And everything Sophia does in Episode 16. In Episode 20 she orders Leila infected with a virus that kills humans quickly and is harmless to her people, in order to mutate it into a form that can be widely dispersed among the human population.
Jetliner Suicide Attack as a weapon in the United States complete with screaming passengers. Obviously NBC's is hoping that nine years was enough for this to just be a credible dramatic threat and not stomach-turning to most of the audience.
The old warehouse collapsing in 1x6.
The episode "Turnabout", in which the threat of a nuclear incident in Southern California is a major plot point, aired a few days after the massive Sendai earthquake in Japan that led to major incidents at several nuclear reactors. In a moment before the President gets updated on the situation, we see him in a meeting with a foreign dignitary... from Japan.