Here is the problem:
1. You want an update
2. To get an update, you need to use the eShop
3. To use the eShop, you need to use the latest system version
4. If you download the latest system version, you can't play roms
5. In order to download the latest system version and still play ROMS, you need emuNAND
6. In order to have emuNAND, you need to use 3.0+
7. 3.0 emuNAND doesn't work with the eShop
8. 3.1-3.3 can brick your system.
9. In order to use the eShop, you need to use GW 2.1
10. Once the update is downloaded, in order to use it you need to use 3.0, which has buggy saves.
Basically, this is what you have to do in order to use an update:
1. Back up your 3ds's SD card
2. Download 3.0 Launcher and place on SD card.
3. Hold L in ds profile and select format emuNAND (this will delete the data on your SD card, which is why you backed it up)
4. Select the first option (GW mode, or if they renamed it something else. Its the red boot)
5. Go to System Settings, verify that it says "GW3D" and if it does, !!!WITHOUT EXITING SYSTEM SETTINGS!!! update
6. Turn off the 3ds.
7. Put your files back on the SD card (it will be 1gb smaller now)
8. Download GW 2.1 launcher and place on SD Card
9. Run ds profile exploit, and select classic mode (second option)
You should notice you have miiverse, as you are now in emuNAND.
10. Enter eShop and search for your update
11. Download the update.
12. Turn your 3DS off
13. Place the 3.0 Launcher back on the SD card
14. Play your game! You should have the update now.
The only downside is you have to use 3.0, which means you have to make sure you can save as well as deal with the system not always running the exploit properly. Basically, you have all the 2.0b1 bugs.
If you go back to 2.0 (GW 1.2) you will not have the update anymore. (On 3.0 you will sill have it)