Well, you did leave NVI Pawniard in as legal in Standard when KSS rotated out.
The big one, though, is that for whatever reason, the 2014 McDonald's set is still legal, which is entirely comprised of cards from KSS and XY, which means there are a LOT of missing cards. The Furfrou alone is in KSS, both halves of the Sylveon/Noivern Trainer Kit, Flashfire and Phantom Forces.
Another big one is the number of older Pokemon reprinted in Generations. There are a LOT of them. (Probably more than half the set is reprints of cards from sets that rotated out, mostly Flashfire and Furious Fists.) It contains (bet I'll miss some):
From XY: Shellder, Cloyster, Pikachu, Raichu (also in the RC), Diglett, Dugtrio, Tauros, Yveltal (RC)
From FLF: Caterpie, Metapod, Butterfree, Ponyta, Rapidash, Geodude, Graveler, Golem, Snorlax, Flabebe (RC), Floette (RC), Meowstic (RC)
From FFI: Magmar, Jynx, Machop, Machoke, Machamp, Hitmonlee, Hitmonchan, Clefairy, Clefable
From PHF: Krabby, Zubat, Golbat, Swirlix (RC), Diancie (RC)
The XY Venusaur-EX and Blastoise-EX, and Combustion Blast FLF Charizard-EX were reprinted as Black Star Promos.
Several older XY Black Star promos have been reprinted as well. (1-3 were in the 2014 McDonald's set, 5 in Steam Siege, 6 in Generations' RC, 13 in Generations, 27 is also Champions Festival (incidentally, you misnamed the BW promo one), 28-30 are the EXes mentioned in my previous point.)
Might have missed some stuff, but that'll probably keep you busy anyway, huh.