Arbitrary Skepticism: Hawkeye was reluctant to believe vampires are real and even more reluctant about Count Dracula (actually King Dracula) being real despite being part of a team that has a god among them. Thor himself brings it up that the others used to consider him a myth before meeting him.
When Steve Rogers and Tony Stark were trapped in the submarine of Red Skull and his minions, with no armour, shield or technology (not even to call the other Avengers), they had to rely on this. They staged being captured, and staged a fight between themselves, with Stark telling Cap that "leaders" exploit the knowledge of the intelligent guys and then leave with nothing... which reinforced MODOC's suspicions about the intentions of Red Skull, and turned against him.
"The Ambassador" has Doom pull one of these to gain access to Tony's database. He got outgambitted.
Comic Book Movies Don't Use Codenames: The Space Phantoms don't actually go by that name; it's just a term Captain America uses to describe them. Even Hawkeye comments on how incredibly cheesy it sounds.
Dracula has much more in common with Baron Blood, particularly his World War 2 background and his connection to Captain America.
The Black Bride (the alternate timeline counterpart of Black Widow) is a combination of Black Widow and Madame Masque, even sporting the latter's iconic golden mask.
The alternate version of Hawkeye is known as Bullseye, in reference the Daredevil foe of the same name.
The Red Skull's monocle and role as the leader of HYDRA come from Baron von Strucker.
Word of God is that the show's version of Ant-Man was an explicit composite of the three men (Hank Pym, Scott Lang, and Eric O'Grady) who have used the name in the comics, which is why his civilian identity is never revealed.
Trick Shot is this mixed with Decomposite Character as well. In the show, Hawkeye was the original Trick Shot before he reformed and joined S.H.I.E.L.D., while the second Trick Shot is his villainous successor.
The Arsenal has a personality much closer to that of The Vision.
Conspicuous CG: There's a lot of blatant CG used for the creation of vehicles, planes, weaponry and buildings.
Divide and Conquer: Cap and Tony figure out that Red Skull's Cabal isn't the unified, well-oiled machine he makes it out to be in In Deep and play on MODOK's resentment at being number two in AIM and HYDRA's hierarchy and Attuma's hunger for power to have them start a little brawl with Red Skull.
Enemy Mine: Skull summons Dracula, Attuma, and Doctor Doom to join him against the Avengers. The first two join up while Doom remains on his own. However, none of the Cabal members particularly like each other, but by the end of "Bring On The Bad Guys", they seem to trust each other to some degree after a major victory came from truly working as a team. Dracula even voices newfound respect for Skull.
Evil Counterpart: Red Skull to Captain America, as per usual. Later he's this for both Cap and Iron Man.
Evil Costume Switch: Played with, after Red Skull jacks Iron Man's armor, he repaints it black and adds the HYDRA logo. The Costume is the same, but the person in it is now evil.
Evil Versus Evil: Doom's and Red Skull's forces fight over an Asgardian weapon in "Serpent of Doom".
Exposed to the Elements: Hulk and Thor have no problems with low temperatures, Iron Man wears his suit, but Hawkeye and the Black Widow are out there in Antarctica wearing the same clothing they always do, and have no problem at all. Hawkeye's suit does not even have sleeves!
For Want of a Nail: "Planet Doom" takes place in an alternate timeline where Doom prevented Tony Stark from being wounded in the Middle East, Bruce Banner from being exposed to Gamma Radiation, and Captain America from being unfrozen. The resulting world has no Avengers or any other heroes, allowing Doom to easily conquer the planet.
Getting Crap Past the Radar: Hawkeye freaking out in Hyperion when other men - specifically big, brawny, ruggedly handsome square jawed men such as the title character and even his own teammate Thor - wink at him.
Hate Plague: M.O.D.O.K. uses nanobots to cause this effect on the Avengers.
Heel Realization: Sort of. In "Hulked Out Heroes" when the others are...well, Hulked Out and acting just like Hulk does when he's particularly angry, Hulk realizes he's not the easiest guy to live with. The other heroes also realize they weren't very understanding of the level of anger and frustration that Hulk has to live with and constantly keep under control.
Heroic Sacrifice: The Arsenal destroys himself in order to stop Thanos from blowing up the Earth.
Hollywood History: "Blood Feud" had a back story of Dracula being a reluctant ally with the Allies in World War II for the sake of defending Transylvania. That is hardly plausible in any historical sense considering Transylvania is literally in the middle of Romania, an ally of the Axis. An explanation can be somewhat made if you consider the fact this cartoon takes a lot of cues from the Cinematic Universe, where HYDRA betrayed the Axis and planned to nuke Berlin, but at no point is this made explicit in the show.
Hypocrite: Red Skull criticizes Iron Man for hiding behind his armor. Then he decides to steal that armor by the end of the first episode.
Inventional Wisdom: In "Mojo World," Hawkeye disables Mojo's hoverchair by hitting an unprotected circuit board on its underside (He even lampshades the design flaw).
I Pulled a "Weird Al": In "Guardians and Space Knights," Cap tells the others their roles in the "just in case Galactus comes back" plan, and Tony tells them good luck with that, but he has his own and runs off. We find that going off on your own is called "Pulling a Stark."
Ironic Echo: The first episode has Iron Man sending holographic images to get the Avengers back together. The Red Skull does the same thing near the end of episode 2 when recruiting villains for his Cabal.
It Only Works Once: Remember how MODOK took apart Tony's armor with his mind in the first episode? He tries again in In Deep only to find out Tony put something in his armor to avoid a repeat of the experience.
Knight of Cerebus: When Hyperion showed up that's when the series started getting darker in tone.
The Leader: The series will have Tony as the leader rather than Cap again.
Legion of Doom: Red Skull will be leading a villain team called the Cabal. He sends invitations to Doctor Doom, Attuma, Dracula (Marvel's Dracula, naturally) and others.
Lighter and Softer: Despite the dark colors and overuse of shading, it still possesses a relatively light-hearted tone compared to it's predecessor.
Tony's narration in the debut trailer borrows heavily from his speech to Loki in the movie, including the lines "Let's do a head count," "The Avengers; that's what we call ourselves," and "We have a Hulk."
Falcon mentions that he's always wanted to meet Captain America, and that he considers him a personal hero. In the comics, Cap and the Falcon were partners for a number of years, and are even close friends.
When Falcon goes to pick up his suit, he calls it "Project: Redwing:". Redwing is the name of his pet falcon in the comics.
Dr Doom being approached to join The Cabal, where he actually did in the comics.
An unfinished suit similar to the Hulkbuster armor from the comics can be seen hanging in Tony's workshop.
Thor is seen wrestling a Bilgesnipe, the creature he was describing to Coulson in the film.
The armored Captain America suit Tony designed for Steve in "Super-Adaptoid" is based off an actual suit Cap briefly wore in the comics during the 90's.
Hawkeye frequently hassles the Falcon over his New Meat status. In the comics, the two dislike each other due to Hawkeye briefly being kicked off the team so that Falcon could have his spot in the line-up.
Statues of Hyperion's fellow Squadron Supreme members can be seen in Episode 7.
After the incident with Hyperion, Thor smashes a mug in celebration like he did in the movie.
In "Depth Charge", Captain America displays some knowledge of Atlanteans after Falcon questions their existence. This may be a nod to his time with The Invaders during World War 2, where he served alongside Namor.
"Bring on the Bad Guys" is named after a reprint book Stan Lee put out in the 70's, which featured the origins of Marvel's most popular supervillains.
In the episode "Mojo World", Mojo's human disguise is his design from Ultimate X-Men.
And Hulk gets outfitted with gladiatorial gear, resembling the Green Scar introduced in Planet Hulk.
Though the character himself does not appear, the title of the episode "Guardians and Space Knights" is a Shout-Out to ROM Spaceknight.
Ant-Man's intense dislike of Hawkeye is a nod to Chuck Austen's poorly-received Avengers run, where Hawkeye slept with The Wasp and ruined his friendship with Hank.
The Iron Legion makes a Big Damn Heroes at the season finale. Although lesser in number than in Iron Man 3, some of the armors resemble the movie-exclusives: the Mark 42 and Igor. And there's War Machine and the Iron Patriot in the lineup, too.
The episode "Thanos Rising" is named after a recent comic book mini-series chronicling the origin of the character.
Never Found the Body: Red Skull is aware of this trope and refuses to believe Iron Man had been killed when Justin Hammer couldn't find his body in Savage
Never Say "Die": In "Thanos Rising," the Falcon finds footage of Thanos destroying Titan, and expresses shock at what he's seeing. The only onscreen acknowledgement of the genocide Thanos committed is a computerized caption stating "Population decreasing.".
New Powers as the Plot Demands: The Avengers member cards in "Depth Charge" rather inexplicably have built in scanners that can instantly identify Atlantaean technology despite never having seen it before.
Noodle Incident: whether this is a continuation of Earth's Mightiest Heroes or not, the team has long since disbanded...for yet undisclosed reasons.
In "The Ambassador", J. Jonah Jameson reports that the "controversial speaker" at the UN is "not Spider-Man... this time."
Not-So-Harmless Villain: Justin Hammer could be seen as this. He did build the Super-Adaptoid after all, and he almost killed the Avengers with it. That's gotta count for something.
Doom seems to slowly be realizing how much of a threat the Cabal really are.
Offhand Backhand: Black Widow, upon calling Tony out to actually lead the team he declared himself leader of, casually backhands a mook trying to get the drop on her.
Off Model: While Tony remotely watches the other Avengers do their hero thing, trying to guess whether how or whether they will succeed Jarvis comments that if Tony were actually betting against himself, he'd owe fifteen billion dollars. This figure is accompanied by a flashing digital display of the number 15,000,000, which for those of us playing at home, is actually fifteen million.
Oh, Crap: The Avengers' reaction to seeing Dracula Hulking Out after drinking the Hulk's blood. They quickly get another Oh, Crap when Hulk turns into a vampire under Dracula's control.
Cap and Tony get another one when they finally take a look at one of the cargo holds aboard Red Skull's command sub and realize that he is building an army in conjunction with Dracula and Attuma the likes of which the world has never seen before; surpassing even their worst fears about what the Cabal was capable of. Amusingly, Skull gets a genuinely huge one when Cap punches Tony.
Cap has this reaction in Bring on the Bad Guys when he realizes the Cabal just busted Hyperion out of prison.
They have this reaction when the Hulk body-checks Odin.
Out of Focus: Black Widow, to the extent that she's missing from the majority of the series. They try to handwave it by saying she also has to work with SHIELD, but it's obvious she was only added to the main cast just because of her membership in the movie.
Plot Hole: In "Blood Feud" vampire!Black Widow TKOed herself by running into a mirror, which Cap says is because she didn't have a reflection. He immediately holds a piece of the mirror up to her to reveal that she does have a reflection. Sure it's fading a little, but it's still visible to anyone who cares to look.
Powered Armor: Naturally, Iron Man. Which Red Skull takes for himself at the end of the first episode.
Power Glows: When the Hulk gets really angry and really strong he starts glowing green.
Tony has a constant golden aura when he serves as Galactus' herald.
Running Gag: Hawkeye's cool purple shades are constantly getting knocked askew on his face.
Hulk doesn't like anyone touching his glass animal collection.
The cookies made by Falcon's mom gets a lot of love.
Sadistic Choice: Red Skull fires two missiles, heavily implied to be nuclear tipped, at Las Vegas and Los Angeles knowing full well the Avengers would be lucky to stop one. And even if they stopped both missiles, he would still get away with the MacGuffin so they served their purpose as a decoy.
Screw Destiny: When the midgard serpent shows up, Thor is sure that he must die in order to stop it, because legends say so. The legend of the Ragnarok, to be precise: Thor will kill the serpent, go nine steps back, and die. All the Avengers rejected the old myths, and took a third option: reopen the portal, and send the serpent back to it.
The Smurfette Principle: As with the live-action movie, Black Widow will apparently be the only female Avenger, at least at the start. For the longest time she was the only female in the entire show, until Sam's mother was introduced. And even then, Widow is absent from the majority of the series.
Spanner in the Works: The Space Phantoms' plan ultimately failed because they didn't count on Falcon's involvement.
Spared by the Adaptation: In the third episode, Sam mentions that his mother baked cookies for the team. In the comics, both of Sam's parents were killed while he was still a child.
Stealth Hi/Bye: At the end of the second episode, Black Widow pulls this off when the team's assembled at Stark Tower.
Look closer: The Doombots that the Punisher flying-tackles are standing just in front of the ledge of a skyscraper; he probably died doing this. Actually a case of Getting Crap Past the Radar.
Lets be honest, when the cartoon was being made to draw fans of the Marvel Cinematic Universe and even replace the team line-up to reflect this, absolutely no one expected Ulik the Troll or Attuma to appear as major villains.
The Arsenal, an obscure character that even comic fans might have a hard time identifying, plays a major role in the first two episodes of Season 2. He even joins the team before pulling a heroic sacrifice.
Vehicular Turnabout: Red Skull and the Cabal actually manage to hijack the Tri-Carrier and use its weapons against the Avengers.
Well-Intentioned Extremist: Hyperion is a genocidal tyrant, but seems to honestly believe that mankind would be much safer under his rule.
What Measure Is a Non-Human?: The Avengers don't seem to have any qualms with using lethal force against the Space Phantoms. Though it's never stated if what they did actually kill them.
They also had no problem using lethal force against vampires either. But being mystical creatures, they probably don't stay dead anyway (or aren't really alive in the first place).
Whole Plot Reference: As mentioned, the character cast and their designs are based on the successful movie The Avengers. The episode "Avengers: Impossible" features an alien invasion of the Chitauri, coming through a portal in the sky, which is stopped when Iron Man manages to send a missile though the portal. Sounds familiar? And what is shawarma, anyway?
The entire first season appears to have been this for the movie, seeing as Skull is revealed to have been only The Heavy, trying to get the Tesseract for his master, Thanos. Thanos likewise makes a brief, silent cameo at the end.
Xanatos Gambit: Red Skull in Blood Feud. He tricks Black Widow into becoming a vampire so the Avengers will fight Dracula, which could end in 2 scenarios beneficial to the Skull: 1) Dracula kills them and gets the super soldier serum, thus ridding Skull of his enemies, or 2) which actually happened, the Avengers beat Dracula, thus convincing him he needs to join the Cabal to defeat Captain America.