Oof. . .yeah.
I can't say I shed any tears for what we lost in Gen 5 simply because what they added there largely felt like padding, but Gen 6 was so barebones in the first place and what little was there felt like it blended so naturally that losing ANYTHING from it is going to hurt pretty bad.
I will say that things like Amie needed a bit of POLISH, though. In a more idealistic world they would remove the less fitting stuff like the Flash-esque minigames during the transition but still keep the general concept of feeding and petting your Pokémon in place.
Yeah maybe if they could work in a bit more Nintendogs and less puzzle with constantly changing picture.
While on the topic, here's a list of things I wish they didn't drop
Gen 2
* Day Night Cycle affected Pokemon rarity
* Weekday events
* Previous region (understandable given how they had to trim Kanto down to fit)
* A rival that makes you want to beat him and his stupid face
Gen 3
* The original Contest format (Only one I got in to)
* Surf that doesn't hurt ally in double battle (only other one I could think of)
Gen 4
* Customizable Pokeball effects
* Pokeathelon
* Game corner (curse you European gambling laws)
Gen 5
* Gym leaders that actually do things outside of Gym Leader-ing
* Seasons
* Actual character development for Rivals