WARNING: NEW 3DS ONLY
OLD 3DS IS TOO WEAK TO EMULATE NEO-GEO AT PLAYABLE SPEEDS

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Current version: 1.5.1

Changelog

v1.0
- initial release.

v1.0.1
- minor fixes.

v1.0.2
- more minor fixes.

v1.0.3
- fixed a freeze when entering sleep mode from the home menu with the game suspended.

v1.1
- added an internal database to recognize games that need a parent rom and warn the user if the needed parent rom is missing.

v1.2
- changed save folder to "sdmc:/retroarch/forwarders/*UNIQUEID*/savefiles" (actually a fix). please move the *ROMNAME*.fs files from the root of your sd card to the new save folder if you wish to preserve your saves, otherwise you can erase the .fs files from the root of your sd card.
- little interface fix.

v1.2.1
- fixed the issue where if the path to the folder selected to save the cia has spaces the program is unable to save it (oops... spaces are the devil).

v1.2.2
- fixed little issue with banner creation (spaces again).

v1.2.3
- interface fixes.

v1.2.4
- fixed a bug where the creator will get stuck at "creating banner" if no banner image was selected.
- another little interface fix.

v1.3
- added option to remap buttons.

v1.3.1
- fixed little bug with the remapping.

v1.4
- fixed parent rom detection, now is has to be in the same folder as the bootleg rom you are selecting (I don't know how I missed this for so long).
- rewrote and revamped a bunch of code for easier maintenance, please tell me if I broke something .

v1.4.1
- fixed little bug were the reset keymap button would incorrectly swap the X and Y buttons.

v1.5
- added random product id and unique id generator. it generates a random code every time you select a rom.

v1.5.1
- added a turbo button. it has to be manually enabled from the button remap option.

Description:
With this tool you'll be able to make independent retroarch cias for your favorite Neo-Geo games using the Final Burn Alpha 2012 NeoGeo core without having to install retroarch or anything besides the generated cia.

Usage:
It's pretty self explanatory, there is only one thing that isn't quite clear:
You need to copy the Neo-Geo bios (named "neogeo.zip") in the same folder as this program.
The program will detect if the bios is usable and wont let you proceed if the bios is missing or incompatible.

If the resulting cia doesn't boot (boots and kicks you out to the 3ds menu without warning) is most likely due to an incompatible romset, you can test your roms with the pc version of Final Burn Alpha or Retroarch before creating the cia to make sure that it will work.

Big games (like Metal Slug 3, SVC Chaos and most of the King of Fighters series) will take a while to boot, just wait a minute and you'll be greeted with the Neo-Geo bios like usual.

Key mapping:
The buttons are assigned as follow:
Neo-Geo A = 3DS B
Neo-Geo B = 3DS A
Neo-Geo C = 3DS Y
Neo-Geo D = 3DS X
Neo-Geo Start = 3DS Start
Neo-Geo Coin/Select = 3DS Select

Turbo button:
As of version 1.5.1 a turbo button has been added. This button has to be manually enabled by giving it a key map from the button remapping option.
It works like a shift button, any other button that you press while holding the turbo button will rapid fire.

Uni-bios usage instructions:

Warning: Spoilers inside!

First, to navigate this menus you have to press A (B in 3DS buttons) to accept/change settings, B (A in 3DS buttons) to change setting in the opposite direction and C (Y in 3DS buttons) to go back.

To access the uni-bios menus you have to press A+B+C (B+A+Y in 3DS buttons) at the first screen (illustrated below).

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The very first option is to configure the region and mode at what the game will run.

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To access the dip switches you have to press B+C+D (A+Y+X in 3DS buttons) at the same screen as before.
Then go to the third option.

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And then the second option.

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You can change the game setting from there like the difficulty, timer, blood and such (most games will let you change difficulty and time from the game menu of you choose to run the game in console mode).

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You can also access an in-game menu that contain cheats if you press Start+Select while playing.

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Download
Alt Link​

Tools used to make this possible:
3dstool, bannertool, ctrtool, imagemagick convert and makerom.
And thanks to @Asdolo for his retroarch fork.