This is a topic I was so waiting for. I hated most of the new cries, because they sounded really bad.
Notable ones that come to my mind are Weavile, Gothorita, Gothitelle, Scyther, Jynx, Flaaffy, Granbull, Teddiursa, Linoone, Lombre, Swablu, Dugtrio, Archeops, Karrablast, Escavalier, Patrat, Taillow, Swellow, Rotom, Gloom, Vileplume, Persian, Trubbish, Garbodor, Pelipper, Masquerain, Hariyama, Drifblim, Delcatty, Electrike, Manectric, Carvanha, Sharpedo, Trapinch, Staraptor, Drapion, Toxicroak, Gliscor, Sigilyph, Tirtouga, Carracosta, Golurk, Braviary, Mandibuzz and Volcarona.
On the other hand, I love how much more hilarious Psyduck, Alomomola and Oddish's cries became in this game. And I don't really mind Pikachu's anime voice being used as it's cry. It's still cute as it is. Chatot however still sounds like its cry was completely unchanged.