Just rewatched the show (IT'S FIVE THIRTY IN THE MORNING. WHY AM I STILL UP). Seeing the interactions between Merlin and Morgana really highlighted all the reasons why Arthur/Gwen grosses me out.
As a disclaimer, I'm not arguing why Merlin/Morgana > Arthur/Gwen. Different strokes for different folks. I'm only describing why I personally enjoy Merlin/Morgana more than Arthur/Gwen.
POWER
To start, I love how Merlin and Morgana are complete equals. In their interactions, they maintain eye contact with each other (and long, smouldering looks to boot) and hold meaningful conversations that go back and forth, neither of them lecturing the other or biting back something they'd like to say but feel is inappropriate just because of who they are. In physical/magical power, they're equals as well.
Arthur and Gwen are NOT equals. In their interactions, Gwen constantly looks down, avoiding eye contact, and her body language is entirely subservient except during her outburst at Arthur, which she quickly remedies by shuttering herself again. As for Arthur, he just talks and talks and talks, while Gwen either humors him or holds herself back. The healthiest interactions they've had with each other so far extend to small talk and light banter, and that's about it. As for physical power, Arthur obviously has his awesome sword skillz, but what does Gwen have? She's great at her job? Ugh, lame.
So why does it even matter if they're "equals" or not? This is where personal preference comes in. I just DON'T think it's cute when two individuals pursue a relationship wherein half the partnership is is accepted as more influential/powerful than the other. It's sick. It's full of mind-fuckery and weird self-confidence issues, exploitation, manipulation, etc etc. In short, it's dom/sub, and not in the fun, kinky way.
ATTRACTION
I love how Merlin and Morgana are drawn to each other by something more than physical attraction or perceived power. They're drawn because they understand each other. Both are hiding their true selves in plain sight, affecting outward personas that they MUST construct. The only alternative is execution, and having such high stakes makes for a thrilling, electric source of bonding.
Arthur's attracted to Gwen because he wants to learn humility and thinks that she can give it to him. Also? BOOBS. As for Gwen, I can't really figure out what she sees in Arthur other than the superficial. He's a good guy at heart? He's hot? Sure, all true and perfectly okay reasons to like someone, but not the stuff legends are made of (and as an aside, I like Gwen/Lancelot much better. They're a boring couple, but totally suited for each other. Very Ron&Hermione-esque). Also, her reactions to Arthur make me wonder if she doesn't have some self-confidence issues or something. I mean, when Arthur's being a dick she's appropriately vexed, but when he does the slightest thing that seems sweet she just GOES for it, beaming and thinking he's wonderful and truly contrite for whatever. She switches between the two emotions so much in 2x02, it just smacks of an abusive relationship :P She's always ready to forgive him, even in the instances where he doesn't deserve it.
In short, Merlin and Morgana have something very real between them as an anchor for a relationship. They respect each other, confide in each other (well, Morgana does, and Merlin wants to), and have crazy nutso magic that is POWERFUL and HOT.
Arthur and Gwen's relationship so far is based on boobs, idealized perceptions of each other, and creepy dom/sub mechanisms.
To glibly address the possible rebuttal that Gwen is perfectly confident and only acts subservient around Arthur because of their stations, I don't buy it. The show is obviously modernized, and the relationships with it. Merlin is a servant too, yet you don't see him being achingly deferential around Morgana or Arthur, right?
Anyway, that is all. It is now six AM and WHY? WHY DID I DO THIS?
To summarize my ships: Merlin/Morgana because it's perfect, Merlin/Arthur because it's hot, and Arthur/Gwen because it's skeevy.