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.
YMMV: Falling Skies
Actor Role Confusion: In the beginning it took an episode or so for viewers who had watched a lot of ER to stop wondering why "Carter" wasn't the doctor.
Ensemble Darkhorse: John Pope. He's gathered a lot of fans, despite the fact even he admits he's a racist, sociopathic anti-hero.
It certainly doesn't hurt that he's often the Meta Guy, calling out Tom Mason and those around him for things that would raise lots of eyebrows if they happened to any other family. (See Trapped by Mountain Lions below.)
Fanon: For the first two seasons (before the harnesses got dropped for other plots) there there were a lot of fans who thought that the harnesses turn humans into skitters. Admittedly harnessed humans have been shown in various states of gray-green skin creeping across their faces, and the harnesses have some absolute effect on their wearers, however there has never been any solid evidence that skitters are changed humans. Karen has been harnessed and heavily used by an Overlord for a very long time yet she still maintains a human skin tone and doesn't show any signs of sprouting extra limbs. As a matter of fact in season 2 the red-eye skitter says that skitters are an enslaved race from another planet. However this has not stopped fans from insisting on the "harnesses turn their wearers into skitters". While the writers continue to leave this ambiguous, the fanon continues.
The Espheni introduce a system of turning adult humans into creatures in season 4, but this is different from the harnessing children seen in earlier seasons.
Fridge Horror: When Anne and Lourdes dissect the Skitter and realize that the Skitters are harnessed.
Jerkass Woobie: Weaver. After we find out what happened to his family, it's hard not to forgive him for his Jerkass tendencies.
Karma Houdini: Hal has yet to be punished for his actions as the (apparent) mole. In fact, most characters have expressed understanding that it was not his fault; only Pope has raised any objections.
We all knew that Pope wouldn't leave Mason to die in the forest.
And that Hal would survive his "surgery" and would be rid of the bug inside him forever.
And that Hal and Maggie wouldn't suffocate to death after being trapped in a room after Lourdes blew up the Charleston HQ.
And that Anne and Alexis weren't really dead.
Scifi Ghetto: An odd case. Whole episodes seem to go by where the whole "invaded by aliens" plot is just in the background as character development takes place, causing a Broken Base. Some fans love the story arcs that focus only on the characters in the show, but the scifi fans get frustrated at the lack of actual science fiction going on in a show with already short (10-episode) seasons. For two episodes straight in season 3, the only aliens seen (skitters, all) only show up as antagonists in very short (thus cheap) CGI scenes as antagonists, and one skitter in a short scene mostly there to hand over the Applied Phlebotinum.
The Scrappy: Lexi Mason. Moral Myopia abounds to the point of hypocrisy. She's definitely some kind of sue with alien powers and everyone on the human side either wanting to understand her or unable to stop her.
Seasonal Rot: The odd directions of season 3-4 make people wonder if this show is just going with the flow instead of leading somewhere. By the end of Season 4, however, they appear to have gotten their direction back.
Trapped by Mountain Lions: Nearly every subplot involving the Mason family. Many seem to think that in a world with humans fighting a war against a technologically superior alien force, the Mason family drama (as well as general hero worship of the Masons) is the least interesting part of the show.
The Untwist: Not too many people believed that Karen really killed Anne and Alexis, so when it was revealed that they were alive in the Season 3 finale, even less people were surprised. It really didn't help that Moon Bloodgood, the actress portraying Anne, was listed in the credits at the beginning of the episode. Also it is worth noting that to kill a major character for real offscreen and simply having it mentioned would have been simply bad writing in averting the Rule of Drama.