Alright, thanks to zoogie and
his tool, we may found a way to install FBI on a 2DS :
Download this pack :
http://jheberg.net/captcha/fbi-injection/
1. Use the gateway launcher.dat to create your emunand (format emunand, backup your sd card content first
2. Setup rxTools :
http://www.rxtools.net/#!howto (replace the rxTools.dat with one of the patched one)
3. Use rxTools to get your nand xorpad (Decryption Options -> Generate fat16 Xorpad). Put it on the FBI injection folder
4. Open emunand tool, choose extract emunand then choose the FBI injection folder for the destination
5. Drag and drop your emunand on dragNandDumpForFat16.bat
6. When it's done (Ignore the error if you get one) , execute decrypt.bat
7. Execute the MAKE_FBI_NCCH which match your console region. It will generate a 0000000X.app file.
8. Open WinImage.
9. Drag and drop the emuNAND.fat16.bin.out on the program then click on OK
10. Go to title/0040010/00022300/content for a EU console or title/0040010/00021300/content for US one.
11. Delete the 0000000X.app inside. (You can extract it first if you want)
12. Click on Image->Inject then choose your own 0000000X.app.
13. Save and close WinImage.
14. Execute reencrypt.bat
15. Restore your emunand with emunand tool.
16. Boot on the emunand with rxTools. Select Health & Safety app. FBI should boot instead.
Tested it on a 4.2 O3DS and it works fine, so it should work on a 2DS too.