Other than the archetypes that have already been mentioned...
Dragon M rayquaza variants will be almost unaffected by the rotation.
Aromatisse variants lose max potion unless it's reprinted, but still seem pretty good. There are other methods of healing they could use, such as super potion or super scoop up, but my guess is it would be more optimal to make use of the space in some other way. I could see florges with sky field become good and I intend to test it. Either way, with all the support fairy has it should still see some play.
Fighting variants lose their best attacker (landorus EX), but still have many good pokemon (Lucario EX, hawlucha, and machamp come to mind), and incredible support. The new machamp EX may be playable in this type of deck, and also note that while the plasma storm zubat rotates out, the phantom forces crobat line will stay in format as well.
While the night march trio will still be legal, the deck will get hit hard by the rotation. I currently play night march/empoleon and from my deck list the cards lost include N, mew EX, empoleon, computer search, Mr. mime, and jirachi EX (which will be replaced by shaymin EX by the time rotation comes). I'm not saying it will be dead, I'm sure it will still see play, but people are going to need to get creative when building decks based around night march in the future format.
The steel or bronzong archetype (whatever you want to call it), is kind of in the same boat as night march.It keeps most of it's support, but loses the keldeo EX/float stone combo, which is a significant blow. M aggron can use mega turbo instead of bronzong, but even he loses victini (which could be replaced by trick coin but it's a lot harder to get into play). Not exactly sure how much we will see of this archetype (unless something similar to the keldeo combo comes out), as I don't see using a switching item being nearly as effective or consistent. I think bronzong is still good energy acceleration and could see some play in another deck within it's lifespan.
Finally, other decks that could appear...
Interesting to note, the venasaur EX/floette deck will still be legal, as will many miltank variants. We may finally see some stage 2 decks (fingers crossed) with the expected drop in Seismitoad EX decks being played. Sorry about the long post, it's a great topic, and I will post again if I think of any others.