Well, I've explained the grunts elsewhere as such - for one, post-game content is only dubiously canonical. Really, the only thing that matters is the main storyline. I, personally, prefer to include the post-game in the canon, but there is nothing that would compel one to do so if they were not so inclined. But for two, assuming that the post-game of B2W2 is canonical, then it could be explained with some simple timescale shuffling. If B2W2 and XY happen around the same time, and if ORAS occurs, say, two or three months after that, then we can have Nate/Rose do whatever in Unova that is outside of Icirrus (e.g. Black Tower/White Tree, southeastern peninsula, etc.) while Brendan/May handle the main plot of ORAS, and then by the time that Teams Aqua and Magma have broken up, a little more time passes, two of the grunts get together and move, and the Nate/Rose meet them in Icirrus. It's a bit of a close shave, but it could happen. There is still the issue with Unova being behind on the types, but I just don't see that as being that big of a deal. Metatextually speaking, it's changed type match-ups forever, but for something that revolutionary, not many people in the games seem to care about it. I recall the Dark and Steel types being similarly swept under the rug. Regardless, the importance of the Fairy type within the story is still dwarfed by Mega Evolution, which has gotten an entire plot dedicated to it in two games now.
So you are right - something is going to be contradicted. But I still believe that a timeline retcon is the cleanest way of going about this.