It may seen like it's building something interesting in the first 10 or so episodes, then at the end it shows that it's just a pile of crap.

The biggest problem of this anime is certainly the pace and the way the mysteries are solved, as well as the solution itself. Very little is actually answered for the first 13 episodes. Then there's the last two episodes that are each one hour and fourty minutes long, and you think "Aha! They will clarify everything now!", and that perhaps the movie-long last two episodes, something quite experimental, show confidence in the artistic direction of this show.
However, it's really not it. These last two episodes give the most dumb explainations for about every single mystery up to that point, and the way these episodes work pretty much confirms that they're only that long because the writer was incompetent to put those answers throught the show, and now they have to shove every little answer to the mystery in an over 2 hours long marathon of expository dialogue between supporting characters.
Giving all the necessary answers for the mystery was very possible without these last two episodes, since there's nothing that crazy or intricate in this story that couldn't be explained in 13 episodes.

Then there's the problem that the resolution for the mysteries are all very unsatisfying and even look "made up in the fly". In a summed up way, a lot of it amounts to "it's all supernatural" and dumb plot-twists that don't make any freaking sense, like the reason for why Key behaves like a robot.
Part of the plotpoints also rely on things that don't have any real-world equivalent, like what the "gel" is supposed to be. Such things really only feel made up so that it's a convenient piece in the story that requires something that can't be naturally answered by anything plausible in a real setting, even with all stretch of symbolism.

Characters aren't memorable. Villains and nice guys all have either loose or underdeveloped motivations. The main villain is a very basic and half-assed executed trope of trans-humanist stories of mega control-freaks.

In the end, this anime only manages to be entertaining in the first 10 or so episodes because it still seems like things will at some point make sense, and that everything up to about that point was curious enough that if given a proper resolution to the mysteries created, maybe the anime could've been actually pretty good. It basically only lives up by expectation alone for a huge portion of it's running time. In the end it all clashes down into a very bad and poorly written story.
Besides that, the anime is pretty well animated (mostly) and has a very nice ambience and thrilling vibe going on for most of it's running time.