Omega Ruby hands down. I think that extra level of polish they can achieve with 6th Gen visuals lends so well to the idea of a living breathing world. There's things the devs can do now that they could never with sprites and that was used to great effect. DexNav revolutionises how to catch pokemon, as for the first time we can see what is waiting in the grass. imo it makes the game flow much better, as I no longer have to go through 10 encounters to find that one Chimecho. I can simply run until a DexNav encounter turns up and decide from there. Makes me feel like I'm actively hunting pokemon, and this is the first time in forever I've been truly inspired to complete a pokedex.
Add that in with all the other brilliant things with the PokéNav like PlayNav as well as some of the virtues of the older region design, like the way routes fit together in a more random, creative pattern than, say, Unova. Despite all my worries, GF married old and new in a very good way.
Ultimately, the Gen VI (and BW2) games have such an impact that they're the only pokemon games I'd nominate for a GOTY award. Innovations and conveniences introduced in these games are quickly making every game before them obselete because of how much better the games a getting.
Honourable Mention goes to Bravely Default. I'd consider nominating it, but it was technically a 2013 game for Europeans. Fantastic even though that second half drags on.