Seasons - While I liked the idea, It was kind of annoying at times. It meant that, unless you changed the date, entire sections of routes/dungeons would be inaccessible to you.
Pokemon following you - I can understand it not returning in Gen 6, but what was stopping them from implementing this in Platinum or Gen 5?
Contests/Concerts - I never really cared about these. It was funny to emasculate the bigger, more intimidating legends, but that's about it. I personally hope they don't lock any mega stones behind these again.
Puddles - I honestly forgot about this.
Fog - This was easily one of the most obnoxious things ever implemented in pokemon. It wouldn't be so bad if GF didn't insist on making HMs require the move deleter to be forgotten.
Customisation - Given GF's history of implementing cool stuff and then removing it without any good reason, I'm sure this is one feature that won't be making it out of Kalos. It's a shame, because this is one of the few things I liked about Gen 6.
Underground mining - One of the best things they ever added and then never included again.
Secret Bases - I personally don't really want to have anything to do with secret bases after having to get a thousand flags to get a Garchompite in Omega Ruby.
Battle Frontier - If they don't include a proper battle frontier I'm skipping out on the next game.
I miss autorun from HGSS. And I miss how experience scaled with the difference between your pokemon's level and the opponent's in Gen 5.