Download links at the bottom of this post.
You need a Japanese 3DS, a Japanese Pokemon X/Y/OR/AS cartridge, and the CyberGadget save device to use this.
If you have trouble running this program, try running it as an administrator.
This is a modified version of the Cybergadget 3DS Save Editor executable that is both in English (though a japanese version is provided as well) and allows for direct editing of one's pokemon x/y save with PKHeX.
You still need a Japanese 3DS, a Japanese Pokemon X/Y/OR/AS cartridge, and the CyberGadget save device to use this.
Use 3DSSaveEditor_en.exe for English, and 3DSSaveEditor_ja.exe for Japanese.
Instructions:
Credits:
Glitch, for providing me with translations for all the strings contained in the cybergadget executable.
Kaphotics, for modifying the exe to interrupt and allow for direct editing with PKHeX.
Downloads:
3DSSaveEditor_en.zip
3DSSaveEditor_ja.zip