Tokyo Ghoul gave me, especially on the two last seasons, a very similar feeling to Darker Than Black. Both series are about superpowers, a single character fighting against an organization and a lot of confusing things going on, which later on (mostly) get clear.
Even though this adaption has been ruhsed, DTB is less rushed. Except at the very end, which is not as harsh as in this anime.
Though the most important part for this recommendation is the mystery feel, on which DTB emphasizes a bit more than TG imo.
It has been some time since i watched D.Gray Man. I'd like to explain why i recommend you Tokyo Ghold to D.Gray Man but i couldnt find the right words.
Its not just the similarity to both main characters. Its the kind of development these two protagonists undergo during the story.
Both anime concern two opposing sides which fight each other. And both protagonists live and fight for both opposing sides.