The Conversion Bureau never made any sense anyway, but here are some places where it would have made less sense.
Not necessarily worlds where the ponies would lose the fight - just worlds where conversion wouldn't logically work.

Before suggesting a World, read the index to make sure I haven't done it already.

"I have sworn upon the altar of God, eternal hostility against every form of tyranny over the mind of man."
-Thomas Jefferson

Three hundred years ago, Equestria tried to assimilate Earth.
They failed. They fled, rather than face justice.
We moved on. We conquered the stars, we made a civilization that spans across the infinite void. We built true harmony between species.
We thought we'd seen the last of Celestia, but as a desperate mobile colony on the fringes of known space came to discover, we were wrong.

It is time to finish what was started by our forefathers.

Based on TCB: Not Alone, by Starman Ghost.

EDIT: Following Starman Ghost's deleting of Not Alone, I've replaced the above link with one leading to a PDF file uploaded to mediafire.

EDIT (14/04/2014): The character of Evening Star was originally created by Starman Ghost. I am using her without his permission.

This story is a sequel to Stardust

Times are changing for Equestria as Twilight’s return brings with it news of people and cultures from beyond the peaceful world everypony knows. Aid and volunteers are freely offered to help the besieged humans of Earth because every Equestrian knows that’s what good friends do. Unfortunately, making friends can also have the unintended consequence of making enemies.

When the monsters besieging the humans strike at Equestria with a level of brutality not seen in over a thousand years, the cry for help is sent to all the kingdoms of the world. Honored allies step forth to fulfill ancient treaties and oaths. Enemies, old and new, bury their grievances. An alliance never before seen in Equestria will be created to combat the monsters from the void.

And because of these events, a grim but welcome sibling to the XCOM project is born.

(XCOM/FiM Crossover)
(Sequel to Stardust, which I recommend reading before starting this. Fortitude Amicitia and Broken aren't required reading but are supplemental to the storyline)
(Gore tag for blood and violence)
(Alternate Universe tag because of the divergence from canon that Stardust has caused)
(Uses elements of Season 4)
(Coverart produced by the amazing Carnelian!)
(Many thanks to Arzoo, BradTheBrony, Vandenbz and Setokaiva for prereading!)
(As of 03/07/2016, the prereading team consists of Arzoo, BradTheBrony, Noble Cause and Metallusionsismagic!)
(Complete with it's own TVTropes page as part of the Stardust continuity. Could use some updating!)
(Character tags will be added as chapters are added!)
(Featured 5/12/2014! Thanks folks!)
(Possible spoilers in the comments! BEWARE!)

This story is a sequel to Stardust

Twilight has finally returned home from the harrowing challenge that Discord set upon her, and the residents of Ponyville and the Elements especially look forward to having their dear friend returned to them.

Twilight, however, has changed. Still suffering from her injuries, almost incapable of using magic and haunted by the memories of her time on Earth, she becomes increasingly withdrawn from those who were closest to her. Will her frustration at her current state and her friends inability to understand her experiences cost her what she valued most before Discord's bet?

(Sequel to Stardust, familiarity with this is recommended!)
(Proofread by Arzoo!)
(Coverart commission drawn by the amazing KairaAnix!)
(Crossover with XCOM: Enemy Within, though the crossover and human elements are minimal)
(Featured 4/28/2014, thanks folks!)

Mort, also known as the Pale Pony (of Death), has been tasked to take time off from his rigorous duties of reaping souls. Seeking guidance, he is directed towards the town of Ponyville, to learn about the magic of friendship from Twilight Sparkle and her friends. All he needs to do is keep his true nature a secret. That shouldn't be too difficult...right?

Special thanks to Specter-Von-Baren and Pyrite Foolsgold for their help in proofreading and editing this story, as I really needed it. Additional thanks to Pilate, Chuckle5, Unimpressive Vagaries and Admiral Biscuit as well! Couldn't have done it without all their help!

Credit for the title card goes to Siansaar, AKA Carnifex.

For another excellent take on Mort, check out Sip's version!

Over a year ago, Equestria began expanding and annexed several nearby countries, and made them a part of the Equestrian Empire.

Several groups have since arisen in order to combat this new regime, to fight against Equestria and restore their countries independence. However, they are no match for Equestria's superior numbers and magic.

However, all of this is about to change as small resistance groups will combine together to fight against the ponies of Equestria, in this tale of epic fights, new technologies, secret conspiracies, unknown magic, and a mysterious entity known only as Zero.

My Little Pony: Friendship is Magic is copyright of Hasbro
Code Geass is copyright of Ichirō Ōkouchi

(Character tags for this story may change over time as I come up with more ideas.)

Featured on 14/04/2014

This story is a sequel to Stardust

When Equestria’s newest member of royalty asks for aid to be offered to her friends from abroad, the best and the brightest volunteer to serve. Captain Steel Song of the Dusk Guard are immediately mobilized to help XCOM defend their world from the enemies that besiege them. However, their first joint operation with the humans takes a turn for the worse and they quickly find themselves fighting for their lives against the full force of the monsters that threaten Earth.

(Stardust/Dusk Guard crossover)
(Coverart provided by a friend of Viking ZX!)
(While familiarity with both stories isn’t required, it is recommended)
(Many thanks to Arzoo for pre-reading!)
(All screenshots can be found at XCOM.wikia.com)
(Featured on 3/13/2013. Thanks everyone!)
(Now has it's own section on TVTropes as part of the Stardust series!)

A crossover with the SCP Foundation - Technically could be read without prior knowledge, but it is just a click away. Why not check it?

Twilight struggles through a slice of Pinkie's mind in the form of a manuscript of her authorship, featuring their lives and adventures through a very different and slightly terrifying perspective.

To what depths will Twilight be forced to plough through? And what is an SCP, and why does being a Brony make you one?

After a falling star crashes into Equestria, ponies all over the world begin to develop a ghostly companion known as a "stand" that grants them strange and unique powers. An attack on Ponyville made by an insane madpony triggers a series of events that sends stand user Twilight Sparkle on a bizarre adventure all across Equestria in persuit of the derranged unicorn that laid waste to her hometown. Based off of the JoJo's Bizarre Adventure manga made by Hirohiko Araki.

Twilight Sparkle is taken into the nightmare of SCP when containment is breached - can she survive?

Cover Art By: Limey-Boy
Based on the SCP Foundation.