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.
Ass Pull: Paradox having a sister wasn't really hinted at at all in the first season, and actually runs somewhat counter to the back-story they gave her. Depending how charitable you're feeling, this is either her being an Unreliable Narrator or the new writers inserting something they just came up with. Fans of the original series are likely to be more forgiving, though, knowing the "Gemini = Twins" thing.
Awesome Music: The opening is a nice sendback to the original opening, which too was pretty awesome. The song starts off nice and sombre complete with a female singer (Shoko Nakagawa of "Ray of Light" fame, who also voices Saori in this series), then kicks off into a rock off similar to the original, even going as far as bringing the original singer for the song into the song.
There's also the second opening, Root Five's "Next Generation" (also called "New Ω Myth", though that doesn't seem to be an official title), which, as a rock/techno take on Seiya themes, manages to trade off a notch of bishonen for a notch of badass while still remaining surprisingly faithful to the concept.
And top of all that, there's the new set of Elemental Powers rules that, depending on your opinon, either gives focus to the mythos or painfully limits the scope of the series.
Some fans of Lost Canvas blame Omega for Lost Canvas not getting continued. Which is full on Fan Dumb because a weekly television series has absolutely no effect on what is an OVA release.
The new season is already causing this. In order:
Key staff members being swapped out for relative unknowns.
The cloths being redesigned again.
Complaining about Shows You Don't Watch: BIG TIME! Some old school fans reach absurd levels of Fan Dumb, bashing Omega just because of the redesigned cloths and because it's not centered on the old 5 Bronze Saints, even though they never watched a single episode. Go to any Forum or Fanpage and have fun with the idiocy.
Ensemble Darkhorse: Taurus Harbinger for his anti-hero traits as well his long story arc in contrast to previous Taurus Saints whose actions were quite disappointing.
Titan is also coming across as one of the most developed villains from the franchise and his duel with Seiya made him more popular. Many wish for him to have a happy ending with Pallas.
Fashion-Victim Villain: Abzu after being removed from Koga. His armor is an asymmetric amalgamation of animal heads, black armor, spikes, and much, much more. Considering that he's a primordial god who birthed life, it's kind of justified.
Foe Yay: A small but increasing amount between Souma and Sonia, especially after he sees how she really killed his father.
From season 2 we have Pallas' obsession with Koga.
Fridge Brilliance: Ever wondered why there is a dark Pegasus Cloth Stone with a regular one when going to commercials? It's a sign of Kouga's use of light and dark cosmo. Epic foreshadowing since episode 1.
Fridge Brilliance meets Parental Bonus: Shiryuu seems to be a happier man after the Mars chapter. While it can be said that he's just happy that his son is safe and the Dark Cosmo infecting him is gone, one can also suspect that he's happy because he finally can do it again with Shunrei.
Growing the Beard: Despite the Downer Beginning, the show's first episodes are relatively light-hearted as they focus on Koga meeting the other main characters and learning how to use his Cosmos. It is when Koga is beaten up by the Director, Mars returns and the main characters start running for their lives that the show starts showing its true colors.
I Knew It: Several fans already predicted Eden's role in the second season during its premiere. It also helped that the opening basically showed people Eden's side.
Shiryu using the Libra Cloth was shown in #77 preview. Many fans knew it would show up after he gave Dragon Cloth to his son and Genbu died.
Iron Woobie: Eden. He's the only member of the main cast to have entered the series with all of his loved ones alive and well. Sadly, this doesn't last. First, his father murders Aria, the girl he loved, before his very eyes. His half-sister, whom he truly cared for and admired, dies after losing control of the Scorpio Gold Cloth. His father dies the instant that Eden finally convinces him of his wrongdoings. His mother is killed right before his eyes when she sacrifices herself in order to keep Abzu's attack from killing him. He pretty much loses everyone he ever cared about in the span of twenty-four hours. He only really looses his composure once, though.
It Was His Sled: Subaru's identity. The openings don't even try to hide it.
Moral Event Horizon: Medea has committed or been responsible for a great number of evil deeds. However, our first real taste of how deep the rabbit hole went was when she callously sacrificed her Love Martyr stepdaughter Sonia, sending her out with a Gold Cloth she could barely handle to die in battle and slightly slow down the advancing Bronze Saints.
Narm: Mars (the god)'s Evil Plan in episode 29 to move Mars (the planet) between Earh and the Sun and thus blot out the Earth's sunlight puts one in mind of a certain other Martian: "It obstructs our view of Venus!"
About 22 minutes into episode 34, Koga is unleashing his dark Cosmo and lets out an angry yell. However, this yell is so brief, random, and abrupt that it can incite laughter rather than a feeling of suspense.
The whole episode about the 10-Minute Retirement of Haruto to become a rock star was intended to be something very serious and dramatic, but some viewers found it to be unintentionally amusing. There is also the scene which shows why Haruto decides to become a singer after listening a song in the radio (Which is the new opening of the series.) What makes the scene so bizarre is that he was listening rock music in the radio seated next to the grave of his friend(and previous Wolf Saint) Yoshitomi. Haruto announces his 10-Minute Retirement to become a singer with this magnificent line:
Haruto: I am no longer a servant of Athena. I am a servant of rock!
The way everyone pronounces Saturn, which sounds like Sataaaun, in a clear attempt to avoid sounding like Satan, which is pronounced very similarly to Saturn in Japanese.
Nightmare Fuel: The ending of episode 25. The results of opening that door were creepy as hell.
It would be quicker to list the aspects of Gemini Paradox' character that is not some kind of Nightmare Fuel. If her gender and Ryuuhou is swapped, she would come off as an extremely disturbing and disgusting man. Which leads to another kind of Unfortunate Implication, since she's the only female Gold Saint.
Case and point: Pisces Amor, the most powerful of all Gold Saints by a mile and Medea's brother, has an infatuation with Yuna. While not quite played to Yandere levels, his persistent advances (to the point of willingly forcing her sit next to him using his powers) still come off as quite unsettling.
Fudou is one distubing saint. His palace was very unsetling with that magma that drains life energy but that's not all. When he dons his cloth and lauches his attack, Nightmare Face kicks in and boy is it creepy.
Abzu himself and Koga tapping into his Darkness element from #49 - 50.
While not a notable scrappy, Seiya was the least popular Bronze Saint from the original manga. Some fans didn't like his hot heated personality, how much damage he can take. In Omega Seiya is instead characterized as Older and Wiser acting as The Mentor without stealing the credit. He was so popular he made it first to the Toei popularity poll from the series. His Big Damn Heroes moments probably helped.
Saori/Athena is infamous for being a Damsel Scrappy. While the early episodes didn't help to deny this, late season 1 shows a scene where she manages to hold a meteor falling to Earth. While that moment lasted shortly, in season 2 she actually goes with the Saints to enemy's place in order to confront her sister. The fact that she manages to fight against Pallas with her Gold Cloth and winning all alone made the episode noteworthy.
Subaru was apparently created to be a scrappy as he was a Butt Monkey and talked a lot. However, he got several episodes that developed his character alongside the other Steel Saints which made the character more appealing.
Arguably, the very concept of Steel Saints. While this particular class of Saints was absolutely hated in the classic series due to being created for the anime, causing them to appear awkwardly in scenes they weren't meant to be in, clearly existing only to sell toys, and then they disappeared mysteriously; in Omega they are shown to serve as the Cannon Fodder of Athena's troops, they hardly take any spotlight as they exist to get shot down, and whenever a Steel Saint is focused on (Ema, Keri), they're well-written and likable. Not being constrained by being a manga adaptation allowed far greater use of this concept.
Ship Tease: Koga X Yuna is very popular in the fandom due to how much time they spend together and due to the fans' desire to include a romantical relationship in the franchise for the first time. During the Sanctuary Arc, fans became happy with the focus on Yuna who was often worried about Koga's mental state. This was even better when Yuna stops Koga from his own darkness by awakening her Seventh Sense.
Seiya X Saori have had a bit of teasing in episode 51 and 53.
The revelation that season 2 (or at least the manga of the same) will include a Steel Saint. General reaction among the fandom can be summed up as "Who let THEM back into the show?"
Said character has already reached Scrappydom all on his own within seconds of his introduction due to being a Jerk AssSmall Name, Big Ego who pretty much just serves as Cannon Fodder in his first actual fight. In fact, he's not only a Scrappy in the sense of being someone whom most of the fanbase dislikes - his whole personality puts one in mind of Scrappy Doo.
Saori, as usual, and for the same reason as always: serving for virtually nothing else than being a Distressed Damsel who needs to be rescued from the clutches of the Big Bad.
So far the "she's the true leader and source of the power needed to deal the killing blow to the Big Bad" subversion hasn't come around yet like it did several times in the original series. Largely because Omega's first conflict isn't even over yet and she started that like some of her original Bronzes did—with a viral case of cosmo-crippling darkness.
Spotlight-Stealing Squad: In Season 2 with Saints and other characters from the older generation having more of the focus than the Omega characters. A vast majority see this shift in focus as an improvement, though.
In the second season, Libra Genbu and Equulus Celeris.
Villain Sue: Pisces Amor, who is able to eliminate without trouble another Gold Saint (Leo Mycenae) on his first apparition. In fact, he was so powerful that only the Physical GodAbzu was able to defeat him.
What an Idiot: Souma. Or at least his decision to go after Sonia alone with no leads on her location at all. When it would be easier for him to stick with the group and wait for her to attempt to capture Aria again or appear at another Cosmo Core which she wants to protect.
I think Kouga and Yuna are exempt from this one. Well, Kouga has a different set of idiot moments.
What Do You Mean, It's Not Political?: One can't help but see Yuna as a character with strong feminist bent, with her defying the traditions for female saints to wear masks. The same defiance can also be seen as a Take That against certain religions with similarly imposing decency law.
Win BACK The Crowd: Or to be more specific win back the Broken Base. People who nitpicked the series just based on the Cloths started becoming nicer with the second season's new designs.
The Woobie: As per tradition of the series, it has a lot.