Doctor Nicholas Rush: Grieving widower who presents a facade of Insufferable Genius because he feels he needs to suffer, and is consumed with his genius and research so much that he can no longer comprehend social behavior? Or arrogant asshat who with one act of arrogance marooned over eighty people on the other side of the universe with a barely functioning ship facing constant danger?
Wray: Obstructive bureaucrat with a hidden agenda or concerned administrator trying to keep everyone out of the way of the politicking of the heads of the military and the heads of the scientists?
The Nakai. Considering how obsessed they are with capturing Destiny, it's possible that their extreme malice towards Humans is because they see the crew as "stealing" the vessel away from them. Since they did not know of it being constructed by the Ancients (or its true mission), after finding out the former information from Chloe and Rush via their mind-probe, they may see their human's claim of inheritance as less valid than their long-standing claim of salvage.
In "Gauntlet", was Eli's claim that he could fix the pod genuine or was he willingly choosing to sacrifice himself to save all of his friends? Alternately, given that he repeatedly reassures everyone that he will be on the other side, was he planning on using the Control Chair to upload himself into Destiny and simply psyching himself to let his physical body die in the process?
Broken Base: From your "more realistic" camps to your "soap opera in space" camps, this series has a divide wider than the Grand Canyon. Even among the people who like the series, there is a gap between Young supporters and Rush supporters; this is probably deliberate, however.
Crazy Awesome: Vanessa running into an electric deathtrap to hit the manual breaker certainly qualifies.
Darkness-Induced Audience Apathy: It's hard to care about the characters in a show whose first episodes exude an aura of hopelessness and mostly contain directionless conflict among the team. This is only compounded because its predecessors were thematically about adventure and prevailing over other adversaries.
Eight Deadly Words: With an entire main cast of characters being thoroughly unlikable, with no "heroes" or even seemingly anyone with any morality to be found, the series quickly fell into this trap. When the series ended with the fates of all the characters being unresolved, many fans were perfectly content never knowing what would happen to them.
Engaging Chevrons: Used when the Destiny is first dialed, but mostly ignored after that. There's also this: "Chevron Nine... Chevron Nine... Chevron Nine..." Makes a return in "Earth" when they attempt to dial, you guessed it, Earth, but one might excuse this as going slow because they were afraid they'd blow the ship up.
Ensemble Dark Horse: Greer in the main cast, Riley in the supporting players. Well, 'till his death in "Aftermath".
Fanon Discontinuity: Many fans preemptively disowned the show as non-canon before it even aired.
Gateway Series: Some of the show's most vocal proponents are people who never watched the first two Stargate series or weren't big fans of them. IGN's Ramsley Isler is one such individual, as is Tycho of Penny Arcade. Some of them, true to this trope, have even decided to start watching the old series just to see what all the fuss was/is about.
Genius Bonus: Anyone who ever learned (or at least glanced) at the Ancient language symbology on the Stargate SG-1 webpage would know that the symbols on the ship's gate are simply numbers, which would make sense for a ship that goes from galaxy to galaxy and would have no common astronomical reference points.
Growing the Beard: Season 2 made tremendous strides forward with the show's formula, trading off much of the criticized Wangst for more action and exploration. "The Greater Good" is commonly seen as a turning point, resolving the ongoing Young/Rush conflict and setting off the series' Myth Arc. And then Syfy canceled it.
Inferred Holocaust: The fate of the alternate crew's descendants from Novus, presuming they weren't all evacuated on their ships. At least one of their colonies had already fallen victim to the Berserker Drones and since they demonstrate advanced reasoning abilities, enough to cut off Destiny from every gate and star in their flightpath, it's very likely that the Novus Generation Ship will eventually come across them.
Coupled with the fact that the Nakai have reached the galaxy as well in their hunt for Destiny and may stick around why they try to figure how they lost its trail post-"Gauntlet". And then there's the Sentient Fungus from "Cloverdale" that possibly may have spread to other worlds. Chances are good that even if the people of Novus do reach their new settlement and meet up with the colonists that the crew rescued, they're pretty much screwed in the long run.
Macekre: The German dub, apart from having atrocious voice acting that did not fit the characters at all, also contained several translation errors, some of whom completely change important plot elements. For example, in the German dub, it is literally said that Destiny is flying "with light speed connected through hyperspace", while actually the exact and complete opposite is true.
Mis-blamed: A lot of fans from SG-1 and Atlantis blamed it for the cancellation of Atlantis. According to co-creator Brad Wright, Universe had been shelved for more than a year because they didn't want to try and run two series simultaneously again, the way they did for awhile with SG-1 and Atlantis, only getting greenlit because Atlantis was on the way out.
In "Blockade", Eli manually piloting Destiny through a Blue Giant, whilst performing on the fly adjustments to the shield.
Moral Event Horizon: Pick one for Simeon: killing Ginn AND Dr. Perry with one action, rampaging through the ship killing and wounding multiple security guards, taking Dr. Park hostage and attaching a bomb to her back, and finally taunting Rush about Perry's death, claiming he (Simeon) left Rush alive so Rush could suffer remorse and guilt Any one of those could qualify, but all of them put together put Simeon far beyond the MEH.
Not to mention it makes things a heck of a lot worse for the other LA members who are genuinely trying to cooperate and play nice.
The galaxy is a truly terrifying place, and it only gets worse with each episode. Chestbursters, giant spiders, and killer bugs, oh my!
Never more apparent than in "Pain" when ticks causing very vivid hallucinations latch onto the Destiny's crew — James hallucinates herself killing Scott, Volker hallucinates being trapped in a coffin, Greer and Rush go Ax-Crazy in an attempt to rid the ship of mutinous civilians and invading aliens respectively, and one Marine tears open his own arm because he thought there were snakes under his skin.
Cloverdale... Sentient plant/fungus that's looks incredibly resilient, aggressive as hell and apparently reproduces by stinging a nearby creature and slowly growing spores inside of it, while turning the host half mad.
Older Than They Think: The backlash that erupted over a character's faith being treated positively. Those involved should take a closer look at Stargate SG-1 season three, where "Demons" has a supporting character from the medieval planet willing to stand up to a Goa'uld-infested Unas thanks to his faith.
Paranoia Fuel: The communication stones. They allow their user to take control of another body over any distance. Of course, it only works if that body has a communication stone of its own, of course, but the potential for abuse is there. Especially if they get hijacked by aliens.
Of course, when SGC starts using it to take over uncooperative allied politicians... well, it's not paranoia then!
The Scrappy: Chloe. The writers recognised her status as The Load and addressed late in Series 1, finally getting her off her ass and contributing something to the team. Series 2 goes at great lengths to make sure she's Rescued from the Scrappy Heap.
Squick: The unfortunate way that Red Shirt Gorman gets sliced by the cloud of alien bugs in "Water". Followed two episodes later by large worm/squid-like creatures that burrow through your skin to eat your yummy insides then eat their way back out. Brrrr.
Strawman Has a Point: Telford's rant makes some sense, at least on the surface, if we consider him a Straw Traitor. It falls apart when you actually take a good look at the people he's arguing on behalf of.
One could argue that Rush was entirely right that Young isn't fit for command. Yes, framing the man for murder was a dick move of epic proportions, but Rush is still their most valuable asset in terms of keeping Destiny functioning and the crew alive. Beating the shit out of him and leaving him for dead was serious Disproportionate Retribution and incredibly irresponsible.
Rush, Wray and half of the civilian crew enacting a coup in "Divided", claiming that they are essentially under a military dictatorship and subject to martial law. When we see that the marines (even Greer) fully prepared to shoot the civilians trapped on the wrong side of the line just for talking back to them, it's hard to deny that Rush and Wray are right. Especially considering that Wray and (begrudgingly) Rush are trying to prevent deaths throughout the entire ordeal.
Future Rush accidentally killing Telford in "Twin Destinies". His reaction is just heartbreaking.
The death of TJ's temporal duplicate from Lou Gehrig's disease in Epilogue
The ending of "Gauntlet", made all the worse by the likely possibility that this is the last we'll ever see.
Park being blinded, apparently permanently.
Riley's death has a major impact, especially how he goes out. And everyone in the crew is hit pretty hard; his death gets mentioned in the next episode, to boot. Furthermore, due to being the one forced to Mercy Kill him, Young suffers a Heroic BSoD and develops a drinking problem that persists for several episodes, before he finally comes to term with what happened.
The deaths of Ginn and Amanda Perry. And then again when Perry and Rush's selfishness necessitate Perry and Ginn's consciousnesses being locked away in different programming, denying them access to the crew any more.
They Changed It, Now It Sucks!: There was already a great deal of complaining that the show would be vastly inferior to previous incarnations of Stargate before airing. Then it aired, and the complaints kept coming.
This is also a potential opinion of the series as a whole. An Ancient ship with mysterious retro-advanced technology, exploring unknown parts of the galaxy with more truly alien creatures and forms of life than the original two series ever had... and the characters are the bunch of the whiniest, least curious, least suitable twerps you could ask for.
During "Seizure", at no point does anyone discuss Langara having been under Ori occupation, nor what happened to Jonas Quinn.
Ugly Cute: The aliens in "Awakening" may be bug people, but you can't deny that first one looks cute while it's curled up in a ball and hugging its legs.
Not to mention the adorable sounds it makes, reminiscent of baby raccoons.
The aliens chasing Destiny actually are somewhat cute. It's just unfortunate they're a bunch of colossaldicks.
The Un-Twist: Telford is a mole. So unsurprising it's surprising.
Visual Effects of Awesome: The ship is a thing of beauty, as is its so-far-exclusive hyperspace window effect. Also, the Stargate surface is so pretty it's hypnotic (and it ain't just down to advances in special effects tech — Stargate Continuum's isn't as pretty.)
As far as the gate is concerned, this is probably due to the much more varied environments and angles we see the gate in compared to previous shows. To initially save money, the gate effect was filmed (for the original SG-1 show) from a number of angles and these stock pieces used over and over.
The Woobie: Everett, Future!Rush in "Twin Destinies", Eli, Chloe, Vanessa