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I feel that way with a lot of the new Pokemon, like Vanillite. It's an ice cream cone, not a Pokemon. Pokemon were originally based on animals, not inanimate objects like a coffin or an ice-cream cone. :/ While I do like a lot of Gen 5 Pokemon, the ones that are based on objects just don't seem...
You should add some things to them, even if it's just something small. Like a sidequest, Pokemon/item that you can't get anywhere else, so there's actually a point in going there. ;)
It was a neat little feature to be able to customise your pokeballs however you want, but I never really used them because I always hated how you had to take them off to deposit your Pokemon in a PC. It just seemed like a waste of time to me.
Yes, I'd really love to see them utilized more. I loved the Triple Battles (Never got to experience the rotation battles), It seemed like a waste to only have a few battles with it. Oh and the first GYM needs a triple battle.