Composite Character: Morgan is paired with King Lot, traditionally the husband of Morgause, another sister of Arthur.
Morgan is also the daughter of Uther and his first wife, whereas traditionally her parents are the Duke of Cornwall and Igraine. In older versions of the legend (as in Geoffrey of Monmouth) Uther does have a daughter named Anna, though her mother is Igraine and thus she is Arthur's full sister. Anna is often combined with Morgause.
Demythtification: While the show has overt magical elements, some parts of the legend are given mundane equivalents.
The Sword in the Stone is rigged by Merlin to release when pushed down instead of pulled.
Excalibur is just an exceptionally well-crafted sword.
There is no magical Lady of the Lake handing over Excalibur. Merlin makes the whole thing up to cover up Accidental Murder at his hands.
Disaster Dominoes: A chain of events in the fourth episode introducing the sword Excalibur leads to two Accidental Murders. While Arthur's new sword is being forged, Merlin dreams of Arthur getting stabbed. The swordsmith wants to present the sword to the king himself, but Merlin rebuffs him since he thinks the smith, an ex-warrior with admitted violent yearnings, might do the deed. The smith takes this as an insult and refuses to hand the sword over. This leads to brawling, and Merlin ends up burning the smith to death when he mentions Merlin's family. The smith's aggrieved daughter snatches the sword away. Merlin chases her to a nearby lake where she plans to discard it. To get to her, Merlin freezes the surface, but then the girl falls in and drowns despite Merlin's efforts to save her.
Eldritch Abomination: Implied. The source of Merlin, Morgan, and Sybil's power seems to be some sort of existential intelligence. This is show-cased by Morgan having 'interactions' with an invisible entity. Or their powers may have simply rendered them bat-shit crazy.
Enemy Mine: As mutual enemies of Uther, Morgan convinces King Lot to create an alliance with her so they can rule Camelot together.
Later, after Morgan figures she'd be better off ruling alone, she betrays Lot's plans to attack Camelot to Arthur. In return Arthur places her under his protection. He even proposes that they rule jointly, but is rejected.
Everyone Can See It: Merlin and Igraine are painfully aware of the forbidden relationship between Arthur and Guinevere and set to put a stop to it. As a result of using magic to find out what lies in Arthur's heart, Morgan knows too.
Evil Counterpart: Morgan is a bit of one to Merlin. Or Merlin is one of Morgan, after Episode 4. Upon her introduction, Sybil to Merlin.
Expy: Leontes is an inverted Lancelot. Like the legendary knight, he is the king's champion and involved in a Love Triangle with Arthur and Guinevere. Unlike the legendary knight, he is actually Guinevere's husband instead of her lover, and it is with Arthur that she commits infidelity.
Extreme Doormat: Igraine starts off as this, which is one of the reasons Morgan detests her.
Foreshadowing: Arthur's dreams about Guinevere. They probably aren't about how they get together, because they already did that, but are probably warnings about how Morgan will take her form and conceive Mordred.
Except Arthur started having dreams about Guinevere before they got together, so it was probably just a foreshadowing of his relationship of her, not necessarily about a liaison with Morgan.
Follow the Leader: It did not go unnoticed that this series started up at the same time Merlin was beginning its fourth season. Though it was probably a coincidence, it also ended up containing several interesting similarities to the other show, including Arthur and Morgan being half-siblings through their father (most versions have Igraine as the shared parent), Morgan having a dark-skinned maidservant, and Arthur being characterized as a Spoiled Brat before his Character Development. These aspects were unique to each show and are seldom (if ever) seen in other adaptations of Arthurian Legend.
Sybil for Morgan and Leontes for Arthur in season finale.
Humiliation Conga: Morgan gets one in the second episode from King Lott. After insulting him in public he hits her in the face, rips her dress open, threatens to rape her in front of everyone and ultimately tethers her to a pole at the top of a mountain. Being Morgan, she gets revenge.
I Have No Sister: Arthur to Morgan in season finale
In the Blood: Despite not having been raised by him and not even knowing they were related for most of his life, Arthur managed to inherit Uther's inability to keep it in his pants. Morgan is as ruthless as her father, but she was at least reared (read: abused) by him before she went to the nunnery.
Left Hanging: The show ends with Merlin leaving Camelot, the construction of the Round Table (with Arthur making a reference to what could have been Galahad and the Siege Perilous, stating that no one can sit in Leontes's seat save the one who is worthy of it) and Morgan visiting Arthur's bedchamber in Guinevere's form which presumably leads to Mordred's conception. Thanks to the show's cancellation, we'll never see how all of this pans out.
Let's Get Dangerous: Igraine, while captured, managed to nearly kill Sybil, stabbed the guard who tried to rape her and escaped.
Light Is Not Good: Sybil is a nun. Yet she has done some nasty things in past and present.
Race Lift: Morgan's maidservant Vivian is of African descent. She is the namesake (at least) of the woman who ensnared Merlin and banished him from the earthly realm, who wasn't. In some versions she's Morgan's agent and in others her role (if not also name) is taken by the Lady of the Lake.
Merlin again. Arthur guesses that Merlin was the one who placed the Sword of Mars in the stone... despite that event having taken place several hundred if not thousand years before the Romans arrived in Britain, since the sword was already there when they showed up.
The legend tells that the sword was placed there hundreds of years ago... but did it really exist for so long? Merlin could have just planted it in peoples' minds using magic and/or his own wiles. However, Igraine and Morgan definitely state that he hasn't aged for a long time.
Spell My Name with an S: Besides the usual spelling choices with Arthurian works, this show's version of Morgan le Fay is called "Morgan Pendragon" (and like BBC's Merlin which has "Morgana Pendragon") unlike the traditional legends where she's not Uther Pendragon's daughter.
Succession Crisis: The core and the main conflict of the series. Morgan is Uther's legitimate child by his first queen, but she is a woman and is therefore not a suitableheir to the throne. Arthur is revealed to be Morgan's half-brother and a potential heir to the throne, directly opposing her.
Uther is poisoned following Morgan putting poison in his soup.
Played with in the third episode. Merlin suspiciously eyes the quail soup brought during dinner, which is received by both Arthur and their host Morgan. Morgan tastes Arthur's soup to prove there's no poison and even dramatically pretends to gag.
Team Mom: Igraine, unlike in the medieval texts where she disappears after Arthur's birth.
Utopia Justifies the Means: Lady Morgan has an unshakeable belief that Britain would be a better place with her as its ruler and she's willing to do anything to get the throne. Merlin's delusional faith in Camelot means that he is capable of anything when it comes to protecting and improving Arthur.
What Happened to the Mouse?: At several points during the series, Morgan is visited by or has visions of a wolf. In one episode, Leontes also has a brief encounter with it. Its purpose is never explained.
Your Cheating Heart: The first time Arthur is shown he is sleeping with Kay's (then) girlfriend. The time after that, he sleeps with Guinevere, Leontes' betrothed. So far, he has only slept with other men's women.
Zen Survivor: Merlin appears to be this. There's something about his bloodstained past and apparent immortality.