Running GBA's e-Reader on the Nintendo 3DS!
This isn't too hard to figure out but I figured I might as well make a guide to make it easy to do.

Note that you cannot use the actual e-Reader due to the fact that the 3DS lacks the GBA cartridge slot.

Spoiler: Using TWiLight Menu++ & GBARunner2 instead of AGB_FIRM injects

If you do not use AGB_FIRM (native GBA support on 3DS) for whatever reason or you are using a DS or DSi, you can also use this guide for TWiLight Menu++ & GBARunner2. Follow Step (2), then copy the e-Reader save of your choice to the directory of your GBARunner2 saves and rename to *I think* ereader.sav or whatever the name of your ROM is.

Requirements:
FBI
GodMode9
e-Reader GBA ROM

(1) Inject the e-Reader ROM into a .cia
You can use Ultimate GBA VC Injector or New Super Ultimate Injector.
Select the e-Reader ROM.

The injectors incorrectly identify the save type.

I got it to work with NSUI using Flash save type.

• Short Name: e-Reader
• Long Name: e-Reader
• Publisher: Nintendo

If you are using NSUI, delete `Banner text (2)`

In case it cannot get the title screen banner, I like to download one from here: http://offlinelistgba.free.fr/index.php

(2) Put the saves on your SD card

Spoiler: Getting your saves

Use a GBA emulator for PC and load the e-Reader "cards". Once all cards are loaded and you have unlocked your game, copy the .sav file and put it somewhere you'll remember. And rename it to the name of the unlocked content.

I am not sure if sharing e-Reader saves are against GBAtemp's ToS. Please let me know if they are OK.
I included Air Hockey-e.sav for now.

The file you may have is "GameBoyAdvance(e-cards)05-April-29"
Assuming that that is your source, extract the following and put them in your SD card.

• Memory Dumps - Mario Party-e (USA).zip
  
• Memory Dumps - NES-e (USA).zip
  
• Memory Dumps - Pokemon Battle-e (USA).zip
  
• Memory Dumps - Pokemon-e TCG (USA).zip
  
• Memory Dumps - Promotional (USA, Australia).zip

I made a folder in the root of my SD card simply called "e-Reader saves". Put your .sav files in your SD card somewhere you can find them.

(3) Install the e-Reader.cia

Spoiler: Open FBI & install the e-Reader.cia

(4) Restoring the e-Reader saves

• Boot e-Reader. You can only modify the save file of the last opened game.
• Reboot into GodMode9 (Power off, then Power + Start)
• Copy the .sav file from your SD card of your choice. ('Y' to copy file)
• Find agbsave.bin in SYSNAND VIRTUAL
• Press 'A' on it, -> AGBSAVE OPTIONS -> Inject GBA VC save

Full tutorial on how to restore GBA saves: https://digiex.net/threads/3ds-gba-save-backup-and-restore-with-godmode9.15395/

Every time you want to "change" the e-Reader cards, you must first boot e-Reader (unless it was your last booted GBA game), then shut down & reboot into GodMode9, then restore save of your choice.

 

[Kikuchi]

I dont see e-Reader.cia for download...

 

[lone_wolf323]

I dont see e-Reader.cia for download...

that's cause its against tos to be posting or linking to warez. It will be found somewhere on the googles.

 

[RandomModderH9]

Does this work for games like pokemon emerald?

 

[raxadian]

Does this work for games like pokemon emerald?

It would have to be the Japanese version as the e-reader support was removed from other versions I think?

But even then there is no currently any form to fake a link cable connection in GBA games running in the 3DS so nope.