Can I point out cliches in my own fanfiction? xD I'll add why I and others use 'em too, I guess.
1- The end of the black org/the unmasking of anokata as a known/loved character. (I continue the Org as a Crooked House faction in Silence, but I wanted to give the story that conclusion that everyone hopes for whenever the baddies in black pop up. I think most fanfiction authors who use this are just impatient for an ending and want to put out their suspicions/hopes on the ending.)
2- Temporary Apotoxin cures. (I didn't want to use a permanent one, as I see it as too oft tied into the former cliche, leaving no loose ends to tie in a too convenient conclusion. I had Haibara give one begrudgingly while the other was a hidden find, but I find them to be convenient ways out for Conan/Shinichi in a lot of fanfiction situations.)
3- New Black Org members/detectives/tie-ins to known characters. OCs, basically. (Erru is one of my favorite OCs. Fiery, sarcastic, strong-willed, and generally in some way aligned with the darker side of the subject matter, I use her to give fanfictions my own twist. I stay away from Canon x OC romance, or romance in general unless it's requested by readers, hence Erru's forever alone xD A lot of 'fangirl' types use OCs as a way of fantasizing that they're with their favorite character/anime love, and others want to use a type of person who just isn't in the canon. Quite a few readers seem to steer clear of anything with OCs, but I never write without them anymore~)
4- Dark turned to light. (True, my reveal of Amuro as a police officer and former ally of Shuuichi and Erru may have been predictable, but I wanted it that way. Gin is a great character, but I couldn't see him betraying the org. to save someone or protect a 'friend.' It's awkward when characters with deep-seated mental issues or obviously ill intentions are forced to undergo a change of heart, but sometimes, with more ambiguous characters, it can be fun/rewarding. I like Bourbon's character, and wanted to use him in Silence as more than an opponent, and wanted to see what I could do with his deceitful nature. And so he's now crossdressing alongside Erru in another syndicate xD I believe a lot of writers have characters they love who are just not on the right side of the law, and to justify their affection, they portray said character as a changed person.)
5- Ran/Kogoro/Detective Boys/Ai in danger. (Quite a few people dislike some or all of these characters, and put them in danger to show them as helpless or unnecessary, or to appease their own hopes of their removal from the cast. Others want to spur Conan/Shinichi into action and use the people he loves, which also casts his enemy in a sinister light and makes you push for the detective despite what you may feel about his extensive lies regarding his identity. I used pseudo-danger, the assumption that the first two were threatened or could be, to get Shinichi to participate in what later twisted into the showdown with Anokata, which he wouldn't have reached without having gotten involved in the issue. I've seen stories in which these dangers are utilized to create a time-limit for our detective, which keeps the readers' hearts racing even throughout monologues and explanations that now serve to draw us closer to the conclusion that is definite. And a definite conclusion, which we lack from Aoyama, is irresistible to many. )
This is my experience/thought. Carry on. xD