Mill should beat Blacephalon every time, at least the Hoopa/Gigas version should. If Blacephalon plays Muk, it's even easier. The only way mill loses to Blace is if they Marshadow the mill player into nothing.
If that doesn't happen, it's pretty easy. Get as many Gigas in play with Ancient Crystal. If the opponent opts to go the all Naganadel route, it'll take four hits to KO Gigas. This is plenty of time to Acerola loop the Gigas, using Mars to dink away resources from the hand. Once they realize the Blace player realizes he can't do this all day, he'll play the Blacephalon and blow you up.
Now, your strategy shifts and focuses on trapping Blace in the Active slot by keeping Energy off of it with Hoopa in front. Search for Lanakila, Plumeria, etc. Mars when you can to try and tick away any Energy Switch or whatever, and...you should win.
If they play Muk, trap the Muk. Keep Energy off of the Muk when they try to Retreat manually, be aware of Energy Switch shenanigans, and you're fine.