First, and most important, are the characters. Merlin and Arthur are interesting characters, at least to me, because of the contradiction within their situations and personalities. Merlin is submissive (almost painfully so) and a servant, but he's also the most powerful character on the show by a mile. Arthur is an entitled bully and a prince, but at the same time he's honorable and, well, also submissive (think about it -- the only person who hasn't successfully told Arthur what to do is Merlin) and he's continually put down by his father. Watching Merlin and Arthur navigate their own internal conflicts is utterly fascinating for me to watch.
Unfortunately, those internal conflicts almost never carry through into AUs. Often Merlin doesn't have any magic at all in AUs (or, if he does, the magic is essentially meaningless to the plot) and thus he's nothing more than a submissive guy who gets pushed around a lot. Arthur is even more boring, since most authors aren't willing to make him an actual bully and thus he's nothing more than a supposedly good guy who occasionally treats his eventual boyfriend like shit for no good reason and who complains. Endlessly. And boringly.
(I should note that Gwen and Morgana usually come out far better, probably because their characters are simpler in canon -- women who kick ass -- and thus are much easier to write.)
Then you have the relationships between the characters. The master/servant relationship between two submissives is actually quite interesting to watch (except in those first few episodes of each season when the show creators try to make Arthur dominant and end up with epic fail instead) -- and while there are times when I want to hit Arthur (a lot), the entitled bully bits mostly serve to emphasize his affection for Merlin. Relationships with Uther and Morgana (and to a lesser extent, Gwen -- sorry, but she hasn't been written consistently and as a result her relationships are inconsistent from week to week) are also fascinating -- Uther is evil and yet he honestly loves his son; Morgana is a million years ahead of her time and is the alpha person in her kingdom and yet has no official power because she is a woman. All of this is absolutely fascinating stuff, even if the show doesn't take full advantage of what it has.
In AUs, however, there's no reason for Morgana not to take over the world, and Uther simply can't be very evil when the worst thing he ever does is berate Arthur for not being good enough. Instead of being a legitimate, layered villain, Uther becomes nothing more than a heavy-handed stereotype who rarely makes much of an appearance because, let's face it, it's not even an interesting stereotype. Morgana, in turn, usually plays the decision maker and planner and while the role suits her, it's not nearly as interesting as being a powerful woman who knows she can do better than the men around her and is nearly self-combusting with her impotence. Meanwhile, Merlin and Arthur are essentially equals in AUs, with any difference in their social status de-emphasized, which makes Arthur's shitty behavior eight hundred times less acceptable and Merlin's acceptance of same eight hundred times more unforgivably spineless.
Finally, you have the universes themselves. Merlin's world, while only addressed on the candy colored surface in canon, has great wells of potential. Genocide. Power struggles. The question of equality. The meaning of honor. The dangers of a bad king. A prince trying to create himself. Impending, inevitable warfare. A surprisingly effective comparison to life in England during the time of Henry the VIII and his daughters, when official religions changed at a ruler's whim and refusing to change with him or her meant potential death. All of these are deep, fascinating subjects that are rarely available to fanfic authors and thus have enormous potential for unique, fascinating stories.
Most of the AUs I've read, however, have had utterly banal worlds: movie rip-offs, university rom-coms, fusions (usually with popular shows that have huge fandoms and thus more than enough stories in those worlds). Nothing that hasn't been seen a million times before and nothing that can show off the characters and their relationships to any interesting advantage. Frankly, these AUs seem to be designed to bury all of the interesting parts of Merlin canon under the weight of mundane plots that have been reused so many times that even putting a new twist on them (a rarely used sport! a not-often mentioned corporate entity!) just emphasizes how utterly done the storyline actually is.
All of this is not to say that it's impossible for there to be an interesting Merlin AU. If authors are willing to really get into the meat of the characters and their relationships and to make an effort to carry that level of detail into a (hopefully interesting and original) alternate universe, there could be a lot of potential for exploration. Unfortunately, however, that doesn't seem to be the choice that most Merlin AU authors are making. *sigh*