[OUTDATED], use AutoLegalityMod from: https://github.com/architdate/PKHeX-Plugins
A Pokemon Showdown Importable To Legit PKHeX Files Converter
The whole project originated from my Smogon Set Database (http://projectpokemon.org/forums/showthread.php?44694-Smogon-Dex-Pokemon-Collection), which made all Smogon Sets for every Pokémon for every tier to PKHeX files, where most also were made legit (by having the data of for example legends saved and replaced and what not).
With the ImportableToPKHeX tool, you can import your Pokemon Showdown Importable and convert them to single PKHeX files, boxdata files or import them into your Cyber Sav file! For the most part, it should give you legal files.
Project Pokémon thread: http://projectpokemon.org/forums/showthread.php?48028-Pok%E9mon-Showdown-Importable-To-Legit-PKHeX-Files-Converter