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By default, the NES VC on the 3DS renders the image in a stretched, 4:3 format and with a dark filter, both of which can't be disabled in any way from the emulator itself. If you're anything like me, viewing images in an ugly and blurry stretched format, and/or having a useless dark filter which prevents the picture from being as bright as it can be, can get really on your nerves. Fortunately, it turns out that this is really easy to fix with CFW and LayeredFS!
Furthermore, this method doesn't require using VC injectors, which mean it can be applied to legit VC titles too!
Actually, I'm going to provide two methods, the easy one, which should be good for most people, and another, harder one, in case you want to tamper with other VC settings.

METHOD 1 (the easy one)
This is the easiest method, and I'm trying to make the guide for this as noob-friendly as possible. So please feel free to ask if there is something that's not clear!
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Requirements:

• Luma3DS (minimum 7.0, although you should always be running the latest version!)
• An SD/microSD card reader / an FTP server homebrew / the microSD management tool (basically a way to access the SD card on a PC)
• The NES VC you want to use this on (already installed on the console)
• FBI (not really necessary, but it makes things so much easier)

Procedure:

1. Download the .zip file attached at the bottom of this post, which contains the files needed for all three fixes (resolution fix only, dark filter fix only, and resolution and dark filter fix)
2. Power up your 3DS, open FBI, scroll down to "Titles", and press A.
3. Wait a few seconds for the whole list to load (takes at most 10-20 secs if you have a lot of stuff installed).
4. Scroll down until you find the VC title you want to apply the fix on, and highlight it.
5. On the top screen, there should be a list of details regarding the title, including the "Title ID", which will be a long string of numbers and letters. Take note of it.
   
6. Power off your 3DS, take out the SD card and connect it to your PC using an adapter (or connect the 3DS to the PC with an FTP server homebrew or the microSD management tool)
7. Navigate to SD:\luma\titles\ (if the "titles" folder does not exist, go ahead and create it).
8. Create a new folder, and rename it as the Title ID you wrote down before, and then open it. You should now be in SD:\luma\titles\<Title ID>\
   
9. Open the .zip attached to this post, and you'll find three folders, one for each fix. Open the folder for the fix you're interested for.
10. Extract the "romfs" directory (the directory itself, NOT the contents) in the SD:\luma\titles\<Title ID>\ folder. It should look like this:
    
11. Disconnect the SD card from the PC and put it back in the 3DS. If you were using FTP/microSD management, turn the 3DS off.
12. Hold the Select button, and while you're holding it, power on the console. The Luma3DS configuration menu should appear.
13. If "Enable game patching" is already enabled, press Start to continue booting. If it's not enabled, scroll down to it, press A to enable it, and then press Start to save and continue booting.
14. Open your NES VC game, and if you followed everything correctly, you will see the fix in action!

METHOD 2 (the hard one)
This method is not recommended since it's harder and doesn't have many advantages. It does allow to access more options regarding the VC, but it's nothing special, although I think savvy people could find it interesting.
Also, since this method is not really intended for noobs beginners, I'm writing it assuming anyone following it already has enough familiarity with Godmode9 and Luma's LayeredFS feature.
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Requirements:

• Same as above except for FBI
• Godmode9

Procedure:

1. Boot into Godmode9, go into the title folder from the SYSNAND SD drive and perform a title search with R+A.
2. When you find the right title, take note of the Title ID while you're there, then select it, select TMD file options, and then select Mount CTX/NDS to drive and navigate to it.
3. Go into romfs and copy the config.ini file to /gm9/out/
4. Plug the SD card in your PC and open the config.ini file.
5. Since the file is getting used for an NES VC title, you can go ahead and delete some lines which contain settings for other systems, namely the [DMG_COLOR], [DMG_COLOR_GRAY], [AGB] and [CGB] sections, and also all the lines below "; DMG Green Mode" and "; Dotbydot DMG Green Mode".
6. The dark filter can be toggled with the "DarkEnable0" option, while the resolution can be toggled under the [NES] group, along with other settings I have not tested.
7. When you're done, copy the modified config.ini in SD:\luma\titles\<Title ID>\romfs\
8. Put the SD back into the 3DS, enable Luma's game patching (if not already enabled), then boot your VC game to test the changes

 

[cualquiercosa327]

Hi,on the second method why dont simply copy the modded config.ini to the place when the original was ?

 

[lAkdaOpeKA]

Hi,on the second method why dont simply copy the modded config.ini to the place when the original was ?

Because GodMode9 doesn't allow writing to mounted TMD images, and that means you would have to copy the title to a PC and modify it there, which I couldn't even find the right set of tools to do it (although I didn't really look much into it), so it's just easier and faster to use LayeredFS

 

[Arecaidian Fox]

Another option if people don't care if they have the original VC title or not is to just make a custom one with the same ROM, using New Super Ultimate Converter or others in the Ultimate Converters series. The tools have options for pixel-perfect and disabling the dark filter.

 

[lAkdaOpeKA]

Another option if people don't care if they have the original VC title or not is to just make a custom one with the same ROM, using New Super Ultimate Converter or others in the Ultimate Converters series. The tools have options for pixel-perfect and disabling the dark filter.

Of course, the guide is for those who want to use official VC titles

 

[Arecaidian Fox]

Of course, the guide is for those who want to use official VC titles

I figured, but you'd be surprised at how many people don't know those tools are there, just trying to provide options

 

[PalindromicBreadLoaf]

Ahh, I never liked how NESVC looked on the 3ds. Thanks a ton for the tutorial, zacchi4k.

 

[Gaspa15]

is there any similiar method for gameboy, gameboy color, gameboy advance and snes?
without using an injector