I haven't seen any ideas for Pokémon games with Kalos Pokémon yet, so here are a few ideas:
Fairy Type doesn't exist and because of this, none of the new pure Fairy type Pokémon (duel-typed Fairies will still be added, but as mono-types) are added (except for Xerneas, who're Normal).
Replaced Pokémon:
Turtwig -> Chespin
Grotle -> Quilladin
Torterra -> Chesnaught
Chimchar -> Fennekin
Monferno -> Braixen
Infernape -> Delphox
Piplup -> Froakie
Prinplup -> Frogadier
Empoleon -> Greninja
Porygon -> Bunnelby
Porygon2 -> Diggersby
Ponyta -> Fletchling
Rapidash -> Fletchindr
Dustox -> Talonflame
Wurmple -> Scatterbug
Silcoon -> Spewpa
Beautifly -> Vivillon
Cyndaquil -> Litleo
Quilava -> Pyroar
Cherubi -> Skiddo
Cherrim -> Gogoat
Mankey -> Pancham
Primeape -> Pangoro
Cascoon -> Furfrou
Drowzee -> Espurr
Hypno -> Meowstic
Hitmonlee -> Honedge
Hitmonchan -> Doublade
Hitmontop -> Aegislash
Porygon-Z -> Inkay
Unown -> Malamar
Kricketot -> Binacle
Kricketune -> Barbaracle
Froslass -> Skrelp
Shroomish -> Dragalge
Natu -> Clauncher
Xatu -> Clawitzer
Shinx -> Helioptile
Luxio -> Heliolisk
Paras -> Tyrunt
Parasect -> Tyrantrum
Pineco -> Amaura
Forretress -> Aurorus
Tyrogue -> Hawlucha
Luxray -> Dedenne
Spiritomb -> Carbink
Celebi -> Goomy
Jirachi -> Sliggoo
Chikorita -> Goodra
Bayleef -> Klefki
Duskull -> Phantump
Dusclops -> Trevenant
Dusknoir -> Pumpkaboo
Breloom -> Gourgeist
Snorunt -> Bergmite
Glalie -> Avalugg
Totodile -> Noibat
Croconaw -> Noivern
Groudon -> Xerneas
Kyogre -> Yveltal
Rayquaza -> Zygarde
Meganium -> Diancie
Typhlosion -> Volcanion
Feraligatr -> Hoopa
It's going to be one big Pokédex featuring Pokémon from BW2 and XY. The Pokémon being replaced are Starters not found in XY or BW2, so legendaries, Swarm mon and Pokémon from White Forrest.
I'm thinking it'll take place in Unova, but with some Kalos elements.