Uranium is definitely one I'd recommend checking out. While it's not quite as dark as Reborn, it does get more mature than the standard Pokemon games, and it has quite a number of fun features!
If you're looking for a storyline-driven game that's also dark, Bonfire Stories is a very fun one to explore. The premise of the game is fairly simple-a group of friends sit around a fire and share spooky stories-but the player actually goes through each story as the protagonist! The stories tend to have a much darker touch, but since they're short stories, there's not much exploration of the characters themselves.
This might not be quite what you're looking for, but Ethereal Gates is a fangame I'd certainly recommend. While not exactly darker in storyline (at least, not yet, the demo has not revealed much about the villainous team), the writing is certainly very nice, and the graphics are really excellent!
Insurgence is certainly another one worth checking out, and the story is certainly much darker than most games. (I personally find some of it a bit excessive, which makes it lose its impact, but it actually has a lighter storyline option-it doesn't remove major events like character death, but it does tone down minor things like ritual sacrifices) Like Reborn and Bonfire Stories, it focuses more on a new look at canonical Pokemon than fakemon. (though it does include some in the form of Delta Pokemon)