Of course such a thing would either require a 'fake gts' setup which allows the games to link the a pixelmon world over wireless but would probably be more complicated then it should be.
The primary route I was thinking of is just import/export a save editor compatible pkm file and use a save editor like pokegen to do the importing or exporting since that might be a lot simpler in the long run.
Whats even better is the pokemon transfered to the games from pixelmon would be considered legit by the games and nintendo if certain factors are met, like location being set to "a distant land"(seems fitting ironically) mainly since most stats, move pools, and other factors already match whats known about the normal gen 6 games so everything would check out.
Only problems I could see are certain legendarys in regards to location.. I mean, if it's possible to import pokemon from gen 1 and 2 games to recent ones with a save editor and they still be considered legit with this method so why not pixelmon? Shoot, I have my original pokemon yellow and crystal teams in my Alpha saphire and sent them thorugh pokemon bank from my pokemon white! If thats not saying "legit" I don't know what will... in other words this would fit pretty well all things considered.
But still not sure how possible all things considered.