Here is a chronicle of fanfics that were rejected for whatever reason. ...Except that my bookkeeping was shitty and countless many rejections were lost to the mists. Oh well, gotta start somewhere.
A Better Boulder - Shipping.
Airborne - human in Equestria, violence
An Infinite Number Of Pinkies - Slow, and way too long for how slow it is.
Celestia and Luna Eat a Hot Pepper - Luna doesn't understand bathrooms and that should be enough for you.
Cheer On - Neither prereader liked it very much. Assorted small things just added up.
Contraptionalogy - Twijack is an awful ship IMO.
Corn on the Cob - Memey, one-note, not particularly funny, poorly edited, Cadence is a loser (this is me making this about my personal opinion on the central character even though I already had two other people reject it for the previous reasons anyway)
Dash's Secret - With this subject matter anything but perfection is a tragedy.
Fallout: Equestria - Patrolling Old Mares' Tales almost makes you wish for a nuclear winter. (violence, based on Fallout which is the least-approvable IP possible, doesn't end with "war never changes")
Fallout: Equestria: Project Horizons - Every new bit I learn about this story just adds more and more crimes to the list. I could make a fucking topic just on the nearly infinite problems this story has. For this topic, though, I'm going with having a poorly-written psyker in a Fallout fanfic. Also endless rape.
Friendship is Mercenaries - Bad Random humor.
Friendship is Optimal - "it's like The Matrix, with horse butts" - Geomancing (has VR horse sex)
It's a Dangerous Business, Going Out Your Door - Several instances of shipping and sexualized content.
Pirates for a Day - Shipping.
The Apple Family - Lesbian gags!
The Cutie Mark Crusade - "bland" is literally all I could get out of Chunky.
Hostile Takeover - So much shipping you'd think it were a merchant fleet. Also other bad things.
Mines of Dragon Mountain - Sequel to Time Lords and Terror, a rejected fic. (and it has its own deaths going on)
Maternal Instinct - Dark, violent content
My Little Alicorn -
My Little Dashie - Creepy premise, takes way too damn long to get to the point, depicts NASCAR as a positive.
My Little Western - Violence
Night Guards - A few little things and then a really big thing I am uncomfortable typing added up.
Past Sins - No Past Sins Clause
Petriculture - Overexplains a gag, makes a character's backstory needlessly sad and convoluted, absurd premise.
Rarity & Pinkie Pie In: The Road to Ponyville - No one liked it at all. I sent it to three people even.
Swayback Mountain - Shipping, smelly.
Time Lords and Terror - Death and Shipping
The Cosby Show: Pudding is Magic - Yarma and Chunky would rage like children if i didn't; also purple monkey dishwasher humor.
The Opener of Ways - Meh quality, bad "ponies learn about bronies" gag just killed it.
The Rainbow Face Up - Sex jokes, mediocre.
The Purloined Pony - Torture scene, otherwise generated little excitement.
Scootaloo Drops Her Ice Cream - A satire of fics we don't have here that cannot stand on its own two feet.
The Star in Yellow - Several RD is a lesbian gags.
Trixie's Revenge - Poor writing.
Twilight's Guilty Little Pleasure - Completely wrong medium. Sets up a naughty situation to subvert it (I hate that shit).
Two & Two & Two - Repetitive, not that great, overexplains a sightgag from an episode. I don't like it.
What if? - What if this fanfic didn't use the word plot in reference to a pony's behind for no goddamn reason?
Whom The Princesses Would Destroy... - had a few things against the rules (the tautological rejection reason)
Wingmares - Where did this sensual massage come from? Where is it going? Why did it have dialogue that wouldn't be out of place in porn? Why am I making this rejection reason rhetorical questions? Will there ever be a fanfic below this one alphabetically to make all these lines seem wasteful and distracting?